Years ago I had an intermittent STL issue that was doing something similar. Damn near drove me to drink. The symptom was a random audio pop, the STL receiver would mute, then the audio would return a second later. The TX site was about an hour drive away, and this happened so randomly, that it took much longer than I'd like to admit to troubleshoot. I finally told the GM I needed to spend the following two days at the transmitter site in a effort to catch what's going on. I literally sat there looking at the STL receiver for hours when I saw it; the signal meter would start to climb above the normal receive level until it pinned at the top of the scale. About the time the signal pinned, the receiver couldn't decode the stream anymore and "POP". I grabbed my spectrum analyzer and started looking at the IF into the receiver. Just before the receiver unlocked, I saw another very hot carrier come up right next to our STL frequency, and literally crawl 5MHz right over the top of our incoming signal, then disappear.
Grabbed the yagi and started walking around the site compound and caught it coming from a building right next to ours. Come to find out, it was a 800 MHz land mobile link amplifier that was getting RF turn-around from another link transmitter. When both transmitters came up at the same time, that caused a spurious mix that was right on top of our STL.
In the end I spent probably ten days up on the mountain solving this problem.