URC actually called me back!  And explained my problem!

It does have to do with the two RF inputs being wired in parallel.  Seems that you can have two RFX-250s (and I assume two RFX-250i) plugged in, one using the 3.5mm phono jack and one using the 3-prog phoenix jack without a problem.  However, you cannot mix them - i.e. you cannot have a 250 in one and a 250i in the other.

BUT...you can mix 250 and 250i receivers if you wire them all to just the phoenix plug.  I tried this and now both the 990 and 990i remotes work.  Great!

But, unfortunately, it did not fix the problem of using two remote at the same time like I had hoped. Pressing button on both at the same time still seems to confuse the MSC-400 :(

So, I might try breaking out a second MSC-400 (or a 350 I have lying around) as a slave to see if THAT config will allow it to happen.