Your better off printing with an SD card anyway so don't worry about the connection issues.

As far as what you're experiencing:

All slicer software will create a header portion of your GCode file (If you open the gcode file in notepad, you will notice that there's a bunch of commands prior to the motion commands (X, Y, etc.).
The header portion is there to tell exactly what's going to happen prior to printing (heating up extruder, heating up bed, homing the printer, etc.).
The header portion that Flashprint will create, will be the correct one for your printer.
If you generate the gcode with any other software, the header will either not be there, or be generic, and thus not compatible with your printer.
So what you have to do is take a g code file generated in Flashprint, open it in notepad, and copy the header portion into the new slicer program *most have an area where you can input custom headers*, that's where you would put that data, and then all your newly generated gcode files will have the correct header.

Don't forget to input all of your printer settings into whatever slicing program you use (extruder size, filament diameter, bed size, etc. etc.)
Hope that helps to answer your question.