I've got a similar issue. I created a a cd with the most recent hotfixes for the end of May using nLite (don't recall specific version, not 1.0 yet, but recent at the time). It was a pretty straight forward configuration: hotfixes, one or two customization options, strip some languages. Any modification to the original install at all was done from nLite. Installed it on my laptop without a hitch. Everything seems to be running just as it should, but I am still plagued by the occasional "Windows File Protection" alert whenever I plug in my USB mouse, install a program with system libraries, etc. Actually using the CD to restore the "system" files doesn't seem to do much good and canceling doesn't really fix the problem either. I even got the alert several times when I was installing a few updates from Windows Update!! any ideas on how to fix this on my running system, or reinstall with a specific config? (i'm not about to turn off WFP since security is an issue)
