Well, an update of sorts. Following the suggestion of reporting "bugs" I did report this. After sending my files I was informed this was "normal". Well, needless to say I'm not terribly happy about that response - since pass-through IR commands work just fine. I don't see how you CI's can put up with this (or maybe not enough have complained). So my advice would be to use pass-through IR commands as much as possible with the remote, and make sure serial commands come first in any MSC-400 macros so that the devices have time to come back on-line (for those that go off-line briefly after they see IR for someone else). I can live with it now that I know what it is and how to get around it...