I have my own custom board definition, from a custom boards.txt, selected. It's an ATMega168 with a clock speed of 18.432MHz.
Not the auto-reset, I'm afraid: I'm resetting it manually, and it works fine with the newer avrdude (both from the IDE and the command line) but not with the "stock" avrdude (both from the IDE and the command line). From the output I posted above, the old avrdude is sending a different command than the newer versions, even with all of the command-line options and configuration files identical. I just don't know why that is, how/if it can be fixed short of replacing the avrdude. If that's the case, I'm wondering if anybody involved with the IDE knows if/when avrdude will be updated in the distribution.