I've tried a variety of bootloaders as well. The Arduino NG has the standard bootloader. The Boardurino has a slightly modified "no-wait" bootloader by LadyAda. The bare ATmega168 was burned directly from a .hex file and had no bootloader.
I'm using a G5 Mac running OSX 10.4.10, but that's probably not relevant the lockups happen even if the Arduino is not connected to USB and running off a separate power supply. I suppose there's always a possibility of build corruption or differences. To eliminate this I just took the code over to an Intel machine running OSX 10.5.6 and rebuilt and re-uploaded the program to the Arduino NG. No difference. Still get the lockups.