Tim, makes sure you only use Buss Type S 25Amp fustats in that transformer. Each size of Buss Fustat has a slightly different shaped base, and they are tapered. This is to stop someone from using the wrong size of fustat. Also dont even try to install a D or P type of fuse as you will muck up the sockets.
I don't know what to say about the odd output readings you are getting... but start with the right fustats and then try again. If the internals are messed up I am pretty sure you would get a warranty replacement if you asked.