The Tools > Programmer menu selection should make absolutely no difference for a standard Upload to a Pro Mini. That menu selection only matters for the Tools > Burn Bootloader and Sketch > Upload Using Programmer. There are some boards that don't support uploading via serial and their board definitions are configured so that the actions you take to normally do a standard Upload operation actually do Upload Using Programmer but the Pro Mini is not one of those boards.
Are you sure the problem wasn't something completely unrelated to the Tools > Programmer menu selection? If this was really the problem you should be able to reproduce it by selecting the USBasp programmer.