If you update twonky and change the path to the program remember to update your plist as well. 

One quick note: When I changed to the zip file version of Twonky server I put the .app version in the trash.  It seems that removing Twonky.app fires a script to remove twonky's settings.  It kept removing /Users/idea/Twonky Library.twonky causing the server to always show as default.  After a restart the cleanup script stopped its insanity and I was able to save the server configuration normally.