I've just received my Atmega32u4 breakout board and as a test I uploaded a simple "blink the boot led" program, with just about no result. No blinken lights for me. While uploading via avrdude through the bootloader went down without a hitch, after a reset and past the boot loader timeout, the little thing just sits there, doing nothing. After trying a few other small test programs with the same result, I decided to try programming it directly via the isp header. And funny enough, that did work.
So, I can upload through the bootloader just fine, but afterwards it doesn't seem to make to my program code, yet when the same program's loaded through isp, it does work. Is this a case of me not reading enough of the fine manual and overlooking something obvious, or is something else going on?