It seems to both depend on the file names, but also the time stamp for the files in question. I can only reproduce it on NTFS partitions, not on FAT partitions with lower time stamp resolution.
I have put two test files here: https://tcmd.madsenworld.dk/attributetest.zip
Inside the attributetest.zip file is a test.7Z - unpack the test.7Z to a NTFS formatted drive. (the reason while I have packed the .7z file in a zip file, is that my Web-hotel provider deletes .7z and .rar files

Mark the two files wcmd_win7amd64_1_eng.ini and wcmd_win7amd64_1_eng.mnu - then open the "Change attributes" dialog and make the "a" box blank in order to remove the archive attributes. After pressing OK the attributes are unaltered in the file panel, you either have to go out and in to the current dir or use cm_RereadSource 3 to have the attribute settings for the two files updated in the file panel.
The same thing happen if I try to set the "a" timestamp again.
If I change the time stamp of one of the two files, I can no longer reproduce the bug.
I can change the file names to for example wcmd_win8amd64_1_eng.ini and wcmd_win8amd64_1_eng.mnu and still reproduce the bug, but if I change the names to wcmd_win5amd64_1_eng.ini and wcmd_win5amd64_1_eng.mnu or if I delete characters in the names, then I can no longer reproduce it.
The bug only occurs if I change the attribute for both files at the same time, not if I change one file at the time.
The bug does not occur when changing the "r", "h", and "s" timestamp - at least not for these two files.
The bug does not occur if I choose more files than these two.
I guess that TC uses some sort of hash to check if the file attributes have been changed and this hash for some reason is the same for these two files whether the a-attribute is set or not. But maybe TC should always update the file list when using "Change attributes" dialog, since there in most cases will be changes to update.