I recently bought a Kinesis Advantage 2. Could you be more specific about how you've mapped Ctl and Option? I mapped Delete and End in the left thumb cluster to Ctl and Option resp. What did you do?
When exported as a text file from the Advantage2, my mappings look like this:
[=]>[`]
[tab]>[\]
[caps]>[tab]
[up]>[down]
[down]>[up]
[`]>[=]
[lalt]>[lwin]
[ralt]>[delete]
[\]>[']
[lctrl]>[lalt]
[delete]>[lctrl]
[rctrl]>[lalt]
[enter]>[rctrl]
[']>[enter]