Learned it the hard way, the two wallets will conflict since they both creating NyanCoin files in your %appdata% folder. You have to back up one somewhere in order to use the other. You can still mine both at once if you use pools though.
thanks!
You can also choose what directory to store each wallet's data! Quoted from https://en.bitcoin.it/wiki/Data_directory (with references to Bitcoin changed):
If you have already downloaded the data then you will have to move the data to the new folder. If you want to store them in D:\NyancoinData then click on "Properties" of a shortcut to nyancoin-qt.exe and add -datadir=D:\NyancoinData at the end as an example:
"C:\Program Files (x86)\Nyancoin\nyancoin-qt.exe" -datadir=D:\NyancoinData