The biggest fault with Reaper is how deep you can go in configuring it.
The best thing about Reaper is how deep you can go in configuring it.
Right now I'm personally going through every instructional video I can find online and the Groove3.com stuff with Kenny Gia (I think that is spelled right) is probably the best instructional videos I have ever watched for any product. I went into it kind of raw and about an hour into the videos I learned that I don't know a damn thing about anything, but I am learning at a fast pace.
Anyway without being in front of it or actually seeing what is going on it's hard to diagnose, but there are a number of settings in the Preferences section and I would really look into things with the sound card settings and making sure that it is set to not release the driver in the background when you are trying to use it to perform. If it is set to release the sound card then it basically shuts down the audio engine whenever Reaper loses focus. Sometimes it's not a big deal and sometimes it completely screws you over because some other app or service or something has taken control and I've had times where I couldn't do anything without closing everything and restarting Reaper and a few times I had to restart the computer.
Another area to look into whether tracks and FX's are set to mute or not playback when they aren't really doing anything. This is great for saving resources, but for a performance you don't want any pops or delays so disable anything that seems like it will slow things down or create a hiccup.
There are also settings for how mutes work; I can't remember exactly what it is called, but basically if you are A/B'ing between two tracks and get a pop or dropout and do not want it then change how mutes work in the preferences. And don't forget that just because you aren't muting the track manually doesn't mean that something behind the scenes of Reaper isn't using the mute function in an invisible manner.
The last thing I'd look into is something called PDC which is plugin delay compensation. It's supposed to help with sync'ing up your tracks when recording with plugins so that you tracks align and you don't have to manually offset the timing by sliding media around, but I think that I read something about it causing some latency issues with others. This is probably the least likely of your issues, but as a relative novice to Reaper myself it really makes me wonder about what else there could be going on in the background that could be causing your issues.
But the first thing that I would look into is making sure that Reaper gets control and keeps control of my audio hardware and see if that helps. That just feels like the most likely culprit to me.
