Compare finds difference in identical folders (and more problems)

[taajo]

I am running FFS 6.15, Build Apr 7 Unicode 64 bit on OS X 10.10.3, and syncing to a NAS server (Linux-based) share mounted in OS X.

I ran FFS to create a fresh copy of a folder with many subfolders. The process finished with no errors. I ran Compare again and it found differences, specifically, that some folders and files in those folders are missing on the target. Visually I confirmed that the files exist on the target with the same size/timestamp. I ran Synchronize (which reported that folders and files were *created*) and Compare again — same folders/files are still "missing" on target. I have "Copy File access permissions" checked in Options.

The source/target structure looks like this:
FolderParent/
FolderA/...
FolderB/...
FolderC/...
FolderD/...
FolderE/...

Say the first Compare after the full copy reported missing FolderB & FolderC. No matter how many times I run Synchronize, Compare still thinks that those folder are not on the target (they are). Then I use Finder to copy those folder to the target outside of FFS. Run Compare, and now FFS thinks that FolderB and FolderC are there but reports that FolderD and FolderE are now missing on the target (those are there!).

Really weird and unpredictable behavior. Does anybody have any ideas?

[Zenju]

Could be related to permissions and/or ownership. Does it help if you leave "Copy File access permissions" disabled?