i could try starting SC manually after windows has finished initiating - would this be worthwhile?
I'm not sure why there should be any problem reading the settings file if the drive is a local one, but if the problem is that the file is not accessible at startup, this might solve the problem.
Please do try that and see if it helps. The other possibility -- if the settings are somehow corrupted during save at shutdown time -- you could try solving by unchecking the box labeled "skip saving settings on shutdown" on the first tab in options.
Again, this should not be happening, but while we are entertaining ways to identify what's going wrong, that might be worth a try. I'd sure love to know what is actually going wrong.