I use the MSC-400 with my MX-980. I have seen several very odd things (besides those mentioned already).
1) There is the 2 command thing (which by the way I have devices that actually work, then when I tried to fix the others, they all broke).
2) I commonly have issues if I try to send out a command more than once a second (single short taps on the button one second apart always work on mine, anything else - not so much).
3) The stupid IR problem (it puts out short burst of IR on ALL the ports before it sends the command you asked for on the correct port, and the MRF-350 does not do this)

If there were something else I could buy and program myself that was as nice as the pair, I'd be all over it, but I really love the MX-980 and RF control so I'm keeping them (and have purchased several)...