1. Are the modules which you can always control from the PC, the very same modules that do not operate when driven by Activehome timers? Yes
2. Can you reliably control the timed modules from PC at around the same times ActiveHome is trying to control the modules by timers? Yes
3. Try plugging your transceiver into the same outlet as CM11 (or the CM11's outlet). Are you still able to 100% control everything using the remotes? With the transceiver plugged into the CM11 socket I can still control 100% using wireless remote. Unfortunately, not able to try it the other way round due to pc location.
If these answers are "YES" then it would appear to be an issue with ActiveHome software. However your description of inconsistent response sure smacks of a possible noise problem....especially either; intermittent noise, or noise right on the threshhold of overwhelming X10 signals.
Must admit that I do have problems with ActiveHome losing communications with the CM11 but is OK when I restart ActiveHome. This may be an issue with the motherboard/Windows XP/serial port. Even so, didn't think that that should affect using the CM11 with comms unloaded and everything stored in the CM11. I get the same inconsistency either way.