I've got a little more detail on what's happening with the equalize function:
If a destination file is newer than it's source file counterpart, then the destination file's timestamp is reset to match the source file's. HOWEVER - the actual destination file itself is NOT modified (but also, NOT copied to the source). (So the files are still different - but with the same timestamp, and now it's impossible to tell which one is legitimately the newer one.)
I've confirmed that it doesn't make a difference which type of drive is the source vs. destination (i.e. USB or HD).
I've got another issue, too, but I'll create a separate topic for it.
Thanks for such a great app!