I guess it must be another problem than Reaper's - for example a conflict with some midi software. Because I experienced it sometimes, and sometimes not. And currently I have it with the M-Audio Oxygen 49 keyboard, no matter which vst host, standalone synth or DAW I try.
Disabling/enabling, resetting, rebooting - nothing works.
Now I am uninstalling all software, drivers etc. again, to see if I can get it connected again. That is indeed annoying to spend so much time again and again only for Windows maintenance, and a good reason to consider a hardware synth for my midi keyboard.
Apparently I spend more time for Windows maintenance than for my piano lessons, but I don't believe that it is caused by Reaper.
Reaper 4.62/Windows 8.1
By the way, even the software that comes with the keyboard, Air Ignite, does not work as expected. They all recognize the device, but can't connect.
P.S. in my case I uninstalled the software CopperLan, and tzhe keyboard works again in Reaper as well as in one other VST host that I tried...
and I am almost sure, most problems that I experienced so far with midi (and sound output) came from some kind of midi tool, Asio or another driver, or their combination. At the moment I am happy with LoopBe, if I need to connect two programs.