I have a similar problem when using Synchronize trying to compare two directories from the command line with a command line of: winsin -Sc:\filedir -Dd:\filedir
in which case the "c" of "c:" is dropped and the "d" of "d:" is dropped.
By changing the command to: winsin -S\c:\filedir -D\d:\filedir
the "c" is no longer dropped, but the "d" is dropped.
Some of the posts seem to imply this is no longer a problem, but I can't seem to get around it.