Are you monitoring the input through the focusrite ("zero-latency monitoring") or through reaper?
What OS/version?
If you can record it and post a .wav somewhere demonstrating the sound it might help diagnostics.
Might be an intermittent process doing something on your computer and interrupting things.
Try what AlfaDude dude said; start by increasing the buffer size to maximum and seeing if it helps.
You could also install
Process Explorer (if on windows) and watch it for processes that appear every 40 seconds, or processes that suddenly use some CPU every 40 seconds. Long shot, but sometimes it turns something up.