Only freezes in X3 for me was with midi routing as well.
I was troubleshooting why I could not get midi out from any synth over to another track.
So I used midi monitor plugins - which I gather have a hard time keeping up if made syncronous, which I don't know.
As long as I let those monitor plugin be disabled though - no problems. Just no action from midi out on synths.
So it might not be the same issue - don't know. Could be these freeware Tencrazy midi fx stuff.
But there are similarities. I was really trying to get a VST midi plugin on another track getting data from synth out.
Summing all things up - it might help narrow down.
Anyway - up you go.