You may need to press the reset button on the Mini Pro to get upload to work - try and time it right! It depends on what sort of USB->serial converter you use.
Did you try holding the reset button down, then releasing it just after the IDE shows "Compiled xxx of 32xxx bytes"?
The other thing might be a mismatch between bootloader and the IDE trannsfer speeds.
What you can do is re-install the bootloader - put on Optiboot - then select Uno for a board type.
That was killing me on a standalone board I had, was selecting Duemilanove for board type after installing Optiboot, NickGammon had me use Uno and it worked great after that.