What happens when you upload under Linux? Can you post the verbose output (hold down shift while clicking the upload button). Do the RX and TX LEDs on the board flash during the upload? What program are you uploading?
It may be a bug in your avr-gcc version that causes the delay() function to work incorrectly. Can you do "avr-gcc --version" on the command line? If it's 4.5.x, that might be the issue.