I have the exact same experience. At first there are brief pauses in sound and response to mouse gestures with or without silence, then the length of the pauses increases to the point that they can exceed a minute. Finally, if you don't quit MainStage and restart it, it crashes altogether.
This problem actually started with Solina V on VC4. I was told a new (paid for) version was coming that might fix the problem, but instead it duplicated it on every plugin in VC5. I have had to disable all VC5 plugins to use MainStage with my VC4 (minus Solina) plugins.
MainStage just released an updated version, 3.2.4, which stated that it addressed some stability issues, and I promptly downloaded it, but it did not help. Using only the Synclavier V plugin, MainStage 3.2.4 still has the same stability, latency and crashing issues that is threaded through all of VC5.
My configuration is a Mac Mini with 3.0 GHz I7, 16 GB RAM, 500 GB Solid State Flash Drive and the built in audio. I have a small 1920x1080 monitor connected to the HDMI port.