Looked at the list of bugs, didn't find this particular issue:
intermittency of successful MIDI signal propagation to new instrument channel.
Just to get this out of the way: REAPER is 5.9.8.2, system is Win 7 (x64) SP1 Home, MIDI controller is an Axiom 61, audio interface is a Saffire Pro 14.
Sometimes, it's a particular VSTi; the track shows the little red line indicating MIDI signal, but the VSTi sometimes won't "wake up" until pressing a key on its virtual keyboard (if it has one), which for whatever obscure reason works.
Other times, there's not even the MIDI indicator signal; if a VSTi has a keyboard or sequencer, those will work- but no amount of resetting all MIDI devices, unplugging/replugging the Axiom's USB connector and refreshing, closing/re-opening the project, or deleting the track and creating a new one, is likely to work.
I've also made sure REAPER's got plenty of memory and HD space to work with, so that's not a factor.
I've tried also switching the MIDI driver from the Axiom to MIDI4ALL, the Saffire MIDI, and even tried LoopBe to see if it would help.
What's got me posting is not that it's a constant issue, but one that's impossible (for me, at least) to predict or pin down and eliminate.
If the very fine folks at Cockos really want to guarantee more converts to REAPER, they might consider designating a larger chunk of time and energy to making this thread a dusty, forgotten relic. It's not NEARly as horrific, but MIDI-as-afterthought was the issue that frustrated me the most with (and drove me away from) ACID, and what I tried to replace ACID with, Sonar X1. Perhaps bad-MIDI-PTSD is coloring my thinking