Hello,
When using the Add Folder button, the Protect Tool also adds hidden system files to the file lists. For example, on Mac OS X the tool adds the hidden Finder database file ".DS_Store" to file lists.
I don't think that accidentally encrypting the .DS_Store file will have an adverse effect although I haven't performed that experiment yet.
If you have the opportunity in the future, would you please consider adding a file filter (or preference) to omit hidden system files with the Add Folder option?
Thanks,
Joe