Hi Dave,
I think this might explain your issue. From the FAQ on this forum:
Q. On the first sync after upgrade from SyncToy 1.4 or 2.0 Beta, where one endpoint is on a FAT16/FAT32 drive (e.g. memory stick or USB key), SyncToy 2.0 wants to re-synchronize all files because the file times look different. What can I do about it?
A. The issue arises from the fact that SyncToy 2.0 has to re-create the folder pair metadata after the upgrade and FAT reports file times in local time and NTFS reports UTC times. There are a couple of *one-time* workarounds to fix this issue:
1) Go ahead and let the folder pair re-synchronize all files (i.e. hit Run on the Preview window and let it complete). This should be ok since you should have done a successful sync before upgrade. This “long” sync will only be required once after the upgrade, since SyncToy will ensure during this sync that the timestamp metadata is reconciled on both sides. After this you’ll start seeing normal SyncToy behavior for these folder pairs.
2) Temporarily change options on your folder pair to “Check file contents” and Run the folder pair. This will only copy the files where the content is actually different – but it will take more time to analyze the files since it will have to compare the file contents. Once this sync is done, you can uncheck the option and continue normal operation.
