Okay, I have verified that, in my corner of the universe anyway, it is is the version of avrdude that comes with 1.0 and 1.0-rc2 that causes the verify issues. No such problem occurs if I switch back to 0022. The verify errors occur with at least 2 different programmers, a USBtinyISP and a pony serial. They both work with 0022 just fine.
But alas, with 0022 I get the null pointer error while uploading sketches using the IDE.