One thing I neglected to mention is that I followed the instructions here: http://blog.psten.de/post/fuel-for-the-stellaris-rocket to stop the launchpad resetting when the 5v supply dropped. This was because when I was experimenting with a large duty cycle for the SMPS the current draw from the inductor was enough to wobble the 5V rail enough to reset the chip. I don’t think I actually needed to do this – it shouldn’t reset now I’ve lowered the duty cycle.
Another thing is that I decided to drop to just 2 47 ohm resisistors in series for each tube as they really were too dim. I strongly suspect I’m now drawing more than the supposed 500mA maximum for a USB device, but only by a little bit, and I’ll be powering it with an old iphone charger that can handle it.