I had the same issue with one of the fobs for my C230 (kept replacing the battery and synchronizing). It turned out that the issue was one of the battery contacts inside the fob was not making consistent contact with the battery. I pulled up the contact with needle nose pliers and it's back to normal. I think what caused it to not be making contact was the fob itself is starting to wear and come loose. Hope this helps, best of luck...
1988 300 SL (5 Speed)
1994 E320 Wagon