Yep, I've seen this, but only in a very specific situation. I had a series of projects that I had started in Sonar 7 - while working on the arrangements, I froze some soft-synths to free up resources temporarily as I was futzing with other bits. When I upgraded to 8.3 and re-opened those projects, anything that had been frozen while working in v7 lost its settings when unfrozen in 8. By the time I realized what was going on, I had already written over the earlier backups. Your experience of creating the sound in one program and then porting to X3 sounds like the same problem.
So now, even though I have *never* had this problem in any other context, I always always ALWAYS export the synth's preset before freezing. I'm also paranoid enough that, before UNfreezing something, I copy the frozen .wav to a new track in case the preset doesn't come back. Hasn't happened, but a little paranoia can be good for you sometimes.