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WinMerge has always worked fine, and now it started glitching. In Windows Explorer, I back up a folder to another hard drive, then I compare them and WinMerge shows them as different. I delete the files, copy them again, this time in WinMerge. Right after the copying, WinMerge shows them as identical, but after I refresh it, half of the files are shown as identical, and the other half are shown as different. All the files shown as identical have a 1-second difference in their dates. All the files shown as different have a 2-second difference. My Compare Method is Modified Date and Size, which I have always used. When I compare "different" file pairs as binary, they are identical. I recreated this issue with 2 different computers, 2 different folders, 2 different hard drives, and 2 different backup drives with 64-bit versions 2.16.50.2, 2.16.44, and 2.16.38. The logs are attached. Please assist. 
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It seems that the drives you’re using might be formatted with the FAT file system. Please try enabling the option However, it’s indeed curious that some files with a 1-second difference were shown as identical... |
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Thank you, turned out the backup drives (which are not mine) are indeed exFAT. The ignore 3 seconds option also worked. |
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It seems that the drives you’re using might be formatted with the FAT file system.
FAT only stores file timestamps with a 2-second precision, so the backup files can end up with slightly different modified times compared to the originals.
Please try enabling the option
Options → Compare → Folder → “Ignore time differences less than 3 seconds.”
However, it’s indeed curious that some files with a 1-second difference were shown as identical...