I've met the enemy and he is me. Looking at various Lissajous pages, I couldn't convince myself that the waveforms I was seeing were even possible. It turns out you can get anomalous results depending on how the scope triggers and how it does alternate mode, vs chopped, along with delays and time-base setting. Ultimately I set up two signal generators, using the TTL out for triggering on one, to explore possible errors. Also did some Lissajous, all at very low frequencies. And then high. Bottom line is I didn't have as reliable triggering on my reference signal (10 MHz GPSDO) as I needed and sometimes "weird" frequencies would appear to be in sync, when they really couldn't be. Now, back to our regular programming.