Jump to content

HELP! I aligned my partitions and now the PC won't boot


Recommended Posts

I can't help it, I like to tinker with stuff, and sometimes I get myself in trouble... like now.  I have a PC dual booting XP & 7, installed on a SATA HDD (using a small FAT primary partition, and the OSes on logicals).  I've read about aligning partitions and thought it was only for SSDs, but apparently not?  Anyway, while booted into Win 7 I used MiniTool Partition Wizard and aligned the partitions on the HDD.  All but the Win 7 partition, as it couldn't be aligned while it was in use.  It asked me if I wanted to restart and have it aligned then, so I said yes.  Upon rebooting it said it couldn't find the boot manager.  Did some Googling, and ended up using my Win 7 installation USB stick so I could access the "repair your computer" stuff.  Tried Bootrec /rebuildBCD, /fixboot, and maybe anther one as well.  There were no issues in executing the commands, but when booting I still kept getting the same message about not being able to find boot manager.  The Win 7 install was fairly new and I didn't have any data I was worried about losing, so I decided to reinstall 7, and this was the first time I noticed that there might be an issue.

Prior to reinstalling, the partitions  looked "normal" in both MiniTool Partition Wizard, EaseUS Partition Master, and Windows' own Disk Management (I had moved the HDD to another PC so I could look at it), but once the reinstall began and I got to the screen where you choose which partition you want to install to I saw 8 instances of unallocated space (all with listed sizes of either 0 or 1 MB).  One between each partition, and also one before the first and one after the last.  I wasn't sure exactly what was going on, but I suspected it was tiny amounts of space that was created when the partitions were aligned.  I just thought it was odd that the programs mentioned above didn't show it and that I was seeing it for the first time during the install.  Anyway, the install seemed to go fine, but upon the first reboot I still got the message about no being able to find the boot manager.

What's going on, and what do I need to do to fix things?  What other info do you need from me?


Edit: Oh, and since I didn't research things as thoroughly as I should have to begin with, is it true that XP doesn't like aligned partitions?  So I need to "un-align" them?  Or start over from scratch and repartition the HDD and forget aligning the partitions?

Edited by E-66
Link to comment
Share on other sites

What exactly do you mean by aligning the partitions? You aligned them by cylinder, by MB or is it something else? And... why did you do it in the first place?:o It's better not to do such dangerous things without a serious reason.

Link to comment
Share on other sites

4k alignment, or whatever it's called that SSD users are supposed to use.  I read that it can also be used on regular HDDs.

Why'd I do it?  I wanted to see if I could notice a performance difference.

Link to comment
Share on other sites

You better clean the disk and repartition from XP install DVD/USB (XP needs cilinder aligned partitions, start LBA is 63). Do not change aligment again this do not work when you have cilinder aligned partitions (XP style), your OS will not boot anymore.

From Win Vista and newer, partitions created during install are MB aligned (start LBA is 2048) which is OK for the "Advanced Format" from about 2012, and you usually do not need to realign partitions anyway.

So as you can see in both cases best choice is do not realign partitions.

Link to comment
Share on other sites

There are no real issues with running XP on a 4Kb aligned disk.

BUT with a VERY notable exception, as soon as you "touch" the XP disk manager to change *anything* it will likely corrupt (not really, only mis-address them) each and every logical volume inside extended.

See here:


Particularly, see:



Most probably right now you have no real choices than to reinstall from scratch, but only because BEFORE asking for help you attempted doing everything (and the contrary of it), after having used - without actually knowing what you were doing - one of these auto-magic do-it-all tools that surprisingly are often not-so-magic and only-do-something.

It would have been perfectly possible to fix the mess BEFORE you attempted the reinstall, and very likely it is still possible, but it implies examining the current situation, correct manually the addresses and fix the various mis-addressing here and there.

If you are game for it, no problem :) we will try and help you, but be aware that it won't be "easy-peasy".

Start by posting an exact view of the layout of the disk, a suggested tool is DMDE:


Post the screen shot of your disk corresponding to this:








Link to comment
Share on other sites

21 minutes ago, jaclaz said:

Most probably right now you have no real choices than to reinstall from scratch, but only because BEFORE asking for help you attempted doing everything (and the contrary of it), after having used - without actually knowing what you were doing - one of these auto-magic do-it-all tools that surprisingly are often not-so-magic and only-do-something.

I'd say that's a pretty good description of the situation. :o

Jaclaz, if I had easy access to you and your knowledge (if you were my next door neighbor, for instance), I would have been more careful in my "experimenting".... but as you can see by the post times, you replied over 18 hours after my initial post.  I had been reading about performance improvements with 4k alignment, read through a few "this is how you do it" articles, had some time on my hands, so I went for it.  "Maybe I should ask Jaclaz about this first" wasn't an option.  I'm a very curious and inquisitive person, and sometimes I lack the patience I should have in particular situations.  I figured the worst it could do was screw up the OS.  My data was safe, so I didn't care if things got ugly.

Everything is fixed now, no worries.  I'll definitely look through the links you posted though.  And thanks for the DMDE link.  I hadn't heard of that program.

Link to comment
Share on other sites

Well, you mean that you would have WAKED ME UP IN THE MIDDLE OF THE NIGHT? :w00t::ph34r:

Be aware that EXACTLY that (having neighbour knock on the door at midnight) is the ONLY case allowing to act non-nicely in my generic Careware license:



Seriously now, the improvement with 4K alignment (on 512 bytes sectored media) is largely the usual over-hyped idea.

Admittedly on "slow" and cacheless devices (such as USB 1.1 or 2.0 sticks) it is noticeable, and - maybe - it could be noticeable on AF 512e drives (though I doubt it, as they are anyway fastish SATA drives AND with large caches).

SSD's (that are overall AF drives) won't also likely get that much noticeable advantage, but it is a very good idea to align to 4k because of other reasons, like the way TRIM and garbage collection works on them and their "page" size.

This post:


touches the matter, the test made here (though a "2048" test is missing):


(which is one of the few I could ever find with some actual data) clears how different partition "alignment" may (or may not) differently better access times OR burst throughput (seemingly hardly both) on different file size ranges, so it is not a "solution for all problems" nor a "one size fits all" solution.

And results may well vary on different devices due to the specific device internals.


On USB sticks, it is usually a very good idea to have aligned partitions (if NTFS) while FAT16/32 need a more complex approach to actually align the filesystem, see these:


Still the advantage, which is very noticeable for booting sticks, is mostly related to when you need to read or write a zillion smallish files, when reading or writing large files there is not that much difference.



Link to comment
Share on other sites

Create an account or sign in to comment

You need to be a member in order to leave a comment

Create an account

Sign up for a new account in our community. It's easy!

Register a new account

Sign in

Already have an account? Sign in here.

Sign In Now

  • Recently Browsing   0 members

    • No registered users viewing this page.

  • Create New...