Bootloader problems

The problem that I am currently having is that I burn the bootloader using my sparkfun parallel programmer and then I am able to use my MiniUSB adapter to load a sketch once. After I have loaded a sketch I can't load another until I burn the bootloader again. The odd thing is that if I load the blink.pde sketch it appears to run fine, but the arduino software is not able to establish sync to the board when programming. Does anyone have any thoughts?

What I have: 2xArduino Mini Pro w/328p 5v/16MHz with regulator and crystal replaced to make it 3.3V/8MHz 2xArduino Mini w/328p 5v/16MHz with regulator and crystal replaced to make it 3.3V/8MHz Sparkfun Parallel Programmer MiniUSB adapter

Well, I may have sorted it out. First of all I set upload.verbose=true in my preferences.txt file so that I don't need three hands to program my arduino. Then I hold the reset button until I get the "avrdude: ser_open(): setting dtr" message it seems to load fine. I thought that the mini pros were supposed to have automatic resets but right now I am just happy that it works.