That's my read, based on OP writing "Got my third dongle, plugged it in and now I am getting SYNC LOSS - BITS PROCESSED in my messages. Unplug the new dongle and it works fine."
@Nate1n22: Sounds like a lack of resources somewhere. How are the dongles connected? Three separate USB ports, or an external hub? Even if they are separate ports on your computer, if there are more available, you may be able to move one or more to different ports that are on different internal USB controllers.
Also, I remember SDRTrunk having an option somewhere that changes how it performs. One setting is supposed to work better (and chew less CPU) with a larger number of systems or talk groups or freqs or something like that. What's your CPU usage look like (Ctrl-Shift-Esc if on Windows)?