Hi there,
There are a couple o settings in Reaper that may be worth tweaking...
First call up the preferences panel (CTRL P) - then scroll down the list on the left and choose 'MIDI Devices' (listed under the 'Audio' category for some strange reason!).
At the bottom of the main panel, you will see tick boxes for "On stop/play..." followed by a few reset options. Clearing the 'Reset CC' should stop Reaper from sending those annoying messages (I think they are enabled by default).
Also look closely at the MIDI Input and Output panels above this to make sure that you have the right things selected; especially if you are using your plugin to edit external hardware. Particularly watch out for any inputs set to "Control" or "Enabled+Control" - this allows external MIDI CC to 'drive' the Reaper mix faders and pan pots, so can sometimes be a source of "rogue" mix changes. Likewise any output set to "Send Clock/SPP" will be sending extra messages that you probably don't want. Just right click on a line in the chart to change the setting.
Also, take a look in the toolkit I posted recently
HERE - there is a MIDI Analyser display in there. Normally it is for use when testing schematics, so it doesn't show on the plugin front panel - but you can make it show up on your plugin's GUI by uncrossing the "Toggle Show in Parent" icon (the little 'eye' symbol on the bar that appears beneath a selected module). You can then pop it into your plugin temporarily so you can get a handle on what messages Reaper is sending.
Alternatively ,you could try my
MagiMIDI tool - that too has MIDI displays, and can also filter and transform MIDI messages; but is probably a bit over the top for what you need to do, and has to be loaded as a separate plugin.
(BTW, those two gizmo's I just shamelessly plugged are total freebies - so if it helps with your design, feel free to pull them to bits and take anything that looks useful).
Hope that gets you up and running. If not, take a peek with one of those analysers and let us know what you see there; that may help give us some clues what the problem is.