Not trying to argue with you here Mitch...more trying to see if I can replicate the issue both in-house (literally) and in the field. I'd say we have a far greater sampling than most as the MX-980 is the only remote we've sold from URC for the past 3 years. We also use this remote with Crestron RF gateways in Crestron systems.
Now granted our systems never utilize IR via line of site for any device and IMO having the programming set to IR/RF is bad juju...and why bother.
That being said you surely will see a bit of latency when using RF via a gateway/processor or base station due to the processing time involved and the time it takes to convert back to IR and send over the emitter. That will always be a longer response time than IR line of sight.
To your point though I'm wondering if when set to IR/RF the remote processes the RF output first and then IR...that could be creating some latency that you are seeing. It's possible the remote can't handle outputting both simultaneously.
Just curious...In your system, are you set to IR/RF but the devices are visible too?