Did you change serial ports? I have a problem with my Windoze box that appears to be a result of the driver for the Belkin USB adapter not handling the RTS line (which is used on the MaxSerial to reset the board and get you back into the bootloader) correctly. When I connected to its onboard RS-232, it worked fine.
Also, make sure you didn't accidentally change the board type: it should be the next-to-last option under Tools->Board, "Diecimila or Duemilanove".
Which bootloader did you install? I bought my chips from Modern Device, and they installed one from Lady Ada. Which works fine on both my Windoze box and my Ubuntu box (which also uses a "real" serial port, not a USB adapter).
Ran