Dear Slimbim: At what point on the flyback are you triggering your acqusition? Depending on how steep the slope is on your sawtooth, you may need to build some kind of comparator, such as one that triggers when it drops to 50% of its amplitude, or some such. I imagine your electron microscope akready has a "real" trigger output available. I'd check the documentation on that first. Also, take a good look at your sawtooth with a wide-bandwidth scope....you might find the rise (or rather fall) time of your flyback isn't all that great! You might need to build a schmitt trigger to speed things up a bit, if you're undaunted by external hardware!
Just a few suggestions.. Eric