I, too, like Repetier's interface much more than the Cura/Pronterface interface. But only because it's more informative and easier to use. What, exactly, was the "trouble" you were having?
Your symptoms are very, very odd. Within the G-code, commands are sent a line at a time telling the printhead where to go next, and within each line, there are both X and Y coordinates (as well as E for Extruder). So we can't theorize that X commands alone are being lost or garbled without also thinking that commands for Y, E, and even Z would sometimes get garbled. Furthermore, each line that's sent is sent with a checksum, so if the command sent from the computer to the printer was garbled along the way, the printer would reject it and ask for a re-send of that line.
Are you putting the very same G-code on the SD card that you were trying to send to the printer thru the Repetier interface?
I wonder if there's some kind of EMI. When you are running the printer off the SD card, is the USB cable still plugged into your computer, with the computer on?
Somewhere back in the early days of this forum, Mooselake published some G-code (and a Simple Basic program for generating said G-code) purely for the purpose of "exercising" the printer's X and Y motion (e.g. to check it for handling ever-increasing speeds, or to check how different values of acceleration work); you might try tracking down that code and giving it a run on your machine.
Are on a Windows, Mac, or Linux computer?
Printrbot Plus operational January 2013
Brass threaded rods (5/16" X 18) & nuts for Z axis
GT2 belts & pulleys
Cable chain to reduce probability of fatigue failure in wires
E3D V5 Hot End, 0.4mm nozzle, also 0.8 and 0.25 in use occasionally
PB fan mount + 40mm fan -- using printed mount adapter, not the E3D supplied fan
Injection molded extruder gears
Optical Z "endstop" (custom designed and built)
Have used many pounds of T-Glase filament. Now also doing some work with Ninjaflex SemiFlex
Print on glass with Scotch Craft Stick or other glue stick