Ok, here are the rather cryptic notes from my random scribblings when I was setting my G-Keys up:

Note: SHIFT+ALT does not trigger ALT, but CTRL+ALT does!

All combinations of CTRL trigger CTRL

SHIFT+ALT doesn't work via G Keys!!!

Modified keys TRIGGER non-modified key!!!!
Make of that what you will (it probably means as much to you as it does to me now!!), but as I said I reckon your original problem is unrelated to Keyclone / G-Keys and more to do with the client's intended behaviour.