One thing worth noting is that window sometimes assigns those "(1)" type terminators when a program tries to place a file in a directory that already contains a file of that name. So if the directory has a song called "Waterloo.mp3" and a program tries to deposit a track called "Waterloo.mp3" in the same directory, windows will sometimes "do a little magic" and append a (1) to the filename to avoid raising a conflict.
Have you checked to make sure that the files you're trying to change don't have duplicate names in their directories? Because attempting to rename "Waterloo(1).mp3" as "Waterloo.mp3" will not work as expected if there's already a "Waterloo.mp3" in the directory. Sometimes with these kinds of file move operations JRiver pops up a "would you like to replace" type box, but JRiver is not consistent in that respect, and many other programs are not either. It's possible that MC is trying to rename and windows is just "helpfully" readding the "(1)" to avoid a conflict!
It may not be your issue, but it's probably worth checking on it to rule it out.