Hello,
I have also experienced this: telemetry works well, but it is nearly impossible to change settings without clicking perhaps 10 or 15 times. After some investigation it turned out our modems were configured in a very suboptimal manner. Almost every time a command was sent from the GCS up to the aircraft, it resulted in a packet collision between the ground radio and air radio. Since they both had similar settings for delays and retries, we would occasionally see 5 or 10 collisions in quick succession, after which one or both radios would give up. This behaviour was easily reproducible on the ground (we initially thought it was poor range in the radios).
Not sure if this is the same thing, but something to look into. We used a logic analyzer to test our setup, but you might be able to try something else. Perhaps you could disconnect the tx line between the autopilot and radio, and instead run that directly to the GCS with an FTDI adapter or something, and see if changing settings is more successful.
For energy control settings, try including conf/settings/control/ctl_energy.xml and conf/settings/estimation/ac_char.xml.
(ac_char.xml returns estimates about the aircraft climb, descent and level flight characteristics).
Hopefully that helps.
Thanks,
-Stephen Dwyer