Anyway I can get them both working together in the mean time? I flick from beta to live ED but can only get EDDI working in one not the other
EDDI 2 should work in live. You'll need to change the netlog path in EDDI's UI but that's all.
Otherwise you'll have to swap out your %APPDATA%\EDDI directory when you move from beta back to live (you did copy it to EDDI-production like I suggested in the OP, right?)