OK, I got some more traces after work. Things look a bit different when we include the left side of the pulse.
Here's one injector cycle with some load on the engine. There is a ~1000 microsecond pre-firing at 14V, then a big negative spike, then the PWM cycles to keep the injector open, then a long discharge.
Here's another single cycle with no load on the engine, showing the same 1000 microsecond pre-fire, and a shorter PWM duration.
This one shows the voltages at different points of the trace. +12V for the pre-fire and the top of the PWM, and -3V (maybe zero) in the noise between PWM pulses.
Here are two firings on the same screen, showing the behavior between firings.
I've also had problems with my kill switch freezing or restarting the MPGuino once every ~10 times I use the switch. It is a big 20A toggle switch wired directly into the injector ground line. I'm not an EE (can you tell yet?), but I suspect it's sending nasty voltage spikes to the 'guino. Sometimes my tach will jump when I kill it, too. Maybe it's time for a relay, or a protection circuit, or a 9v battery power backup circuit like someone here did...
I'm enjoying this learning experience, thanks for your help!