EoC via ignition switch possibly bad for electrical systems?

[Ecky]

This tank I've been trying to work a bit of EoC into my driving, and I noticed some odd behavior with electronics. I haven't built an injector kill switch yet so maybe it's in the nature of using the ignition switch, but at one point when I turned the ignition back on and bump started it, I lost the left channel of my radio (I have an amp in the trunk), and later in the drive my MPGuino froze up on me and had to be unplugged and rebooted. The left channel didn't start working again until I had parked the car an turned it off - next time I started it everything was ok.

Is flipping the power to everything in the car like this ok? Will this be resolved once I build a kill switch? I'll still be jumping between ~12v and 14v.