I've also noticed that with latest winrar clrmamepro does not wan't to remove files inside rar files but packing works good.
I'm encountering this as well, with WinRAR 5.01 x64 and clrmamepro 4.012 x64. It does not occur in clrmamepro 4.011a with WinRAR unchanged.
I've built a test dat and then rarred the files in various ways. (Dat attached, rar files
Here.) Extract the rar files from the zip to a folder and then rebuild the dat with that folder as the source and "Remove Matched Sourcefiles" checked.
Rebuilding under clrmamepro 4.011a, everything behaves as expected. file5 is deleted from the rar file but the rar file itself is not deleted because it contained other files. file6's rar file is untouched because it is a multi-part rar file that contained other files. All other rar files are deleted.
Under clrmamepro 4.012 however, the results are different. file1 is deleted from the rar file, but the rar file itself is not deleted leaving a rar file containing only an empty folder. file2, file3, file4 and file6 are not deleted at all (Produces warning message: "can't remove file(s) from..."). file5 is the only one that is deleted in the same way as under 4.011a.