Travis;
In your original fused configuration, if you drop a leg (blow a fuse) it may cause some kind of surge. I have always been warned against fusing single line input to the amps. Give it a try and hope it helps.
On another subject, I'm trying to install Linuxcnc on my old router with dyn2 drives and 750 watt motors. Would it be possible to get a copy of your ini and hal file? I'm trying to learn this op system so anything I can get my hands on is appreciated.
Good luck.
Bill