This note was originally added to IE Version 5, but may be relevant to all versions.

Don't run IE on an RW mounted DOS partition !
Pretty problematic directory renaming/corruption can happen.
This seems to happen if Wine doesn't have access to certain Windows registry keys.
Renames e.g. "Program Files" to "$!$!$!$!.pfr" and does other horrible things.
BTW, it does not only happen with IE, as it seems to be a generic Windows Setup process of Explorer which is doing this, which can be launched under multiple circumstances.
To be safe, use a backup copy only, i.e. copy all relevant windows files over e.g. to an ext2 partition.