I assume, you have extracted the MenuSingle from an unmodified copy of the game, which only has the original eight cup icons.
CTGP-R patches the MenuSingle before loading the game, so it can be used properly - but once another MenuSingle exists in your MyStuff folder, it will overwrite the patched version afterwards, thus this happened.
In conclusion, I wouldn't really recommend editing the MenuSingle while using CTGP, especially when you're too inexperienced and mind the playability.
There are some patched templates around, but I haven't tried them out on my Wii with CTGP yet.