I just replaced my old Onkyo reciever witha new TX-SR607 reciever. I am happy with it in every aspect except remote control. It works perfectly with the remote supplied with it but it doesn't have the capability of turning on/off three separate units at the press of one button like I was capable of with the old reciever with a Comcast three unit remote and also a Sony RM-AV2100B (I promised the wife it would be as easy to use as the old setup).
Onkyo supplied remotes for models below the 7xx series generally don't support macros nor are they learning capable...just as you've discovered.
With one code the Comcast remote would turn it on, but not off and another code would turn it off but not on. I tried the Sony remote without results.
This is likely because the Comcast remote is a pre-programmed remote, the kind where you enter a 'setup' code to load a table of various remote commands into memory. There may be multiple setup codes listed and they may overlap (meaning one setup code controls most functions and another controls other functions the first didn't but no longer controls some of the things the first code did). Pre-programmed remotes rarely ever work nicely for all functions.
Onkyo goes back and forth between supporting discrete power codes (different code for on and off) vs toggle power codes (one code turns it on and off). The last few models have gone back to discrete codes and it sounds like yours is that way. The Comcast remote probably has only toggle codes.
The solution is simple...if you're willing to spend a few bucks for a real universal remote control. I'm a fan of URC remotes and use the MX-350. Other members rave about the RF-20 which is quite a bit cheaper (like under $100 for the remote AND the RF basestation) and for all intents and purposes is pretty much the same (some minor features on the MX line are left out of the lower cost version).
Buy one of those and teach it every single command from every single remote you have and then put the orignal remotes in a drawer. I haven't used more than one remote for at least the last five years.