Good news! Gerry, you convinced me that the flash plugin was the place to look to fix the problem. It turns out that firefox was seeing two versions of the flashplugin, and even though one was disabled according to the firefox add-ons/plugins dialog box, it seemed to cause issues for x2go. I uninstalled, the old plugin completely (deleted its libflashplayer.so), and kept the other one (which happened to be the most recent version, 10.1r102). Now the flash program runs properly via x2go!
Thanks, Gerry!
By the way, you said that the flash plugin pegged your CPU. Were you still able to view the flash program, and slide the slider to see the various scales? It works fine for me now, both natively and in x2go.