I'm running the G15 Profiler software as administrator.
I've set it to persistent profile, prior to that I could have the G-Keys for only one instance of wow.

I'm running Keyclone with (2), (3), or (5) accounts at once, with keyclone opening them for me.
Keyclone is run as an administrator as well.

I'm not having your issues, but not sure exactly how a G13 differs from a G15.
A PM to Keyclone is your best bet.