I'm going to be honest, I use guildwork and run multiple instances and I actually have not run in to any issues in a long time. I did hear recently some of my friends are encountering issues with crashing since the last patch or so.
That's exactly what happened!
Only thing I can see is that it's causing errors with another plugin or addon.
Edit: I turned off the Shout injection in the guildwork settings on the guildwork.com and the constant flooding and duplicating of shout messages have stopped.
It still crashed 10 minutes later.