I have the same issue, with the same settings as Harry. But I have some more observations that may help:
When I turn the enhanced taskbar off in startallback config, and have it restart explorer. The taskbar has color X (which is set in Windows). When I turn it back on taskbar dissapears, comes back with color Y, and then turns transparent. Color Y is the color that is set in startallback as custom taskbar coloring.
I've used ClassicShell before, and then migrated to startallback
Hope this helps =)