I have a Printrbot Plus also.
In Repetier, there is a menu item called "tools" which gives you a calculator for calibrating according to which belts you are using. Assuming that you are using the same belts for X and Y, then your calibrations should be extremely close to identical. For example, I am using a belt pitch of "2mm (GT2 Belt)" and a pulley with a tooth count of 20. So this gives me 80 steps per mm. After extensive work calibrating rectangles inside and outside dimensions, I ended up using 81.1 for both X and Y. That's just a shade more than 1% greater than the theoretical value - and it's probably because I was overriding Slic3r's automatic generation of trace width with a wider one. So what I'm saying is an excellent place to start is with the exact theoretical values, and keep X and Y identical.
Now, to put this into practice, use Repetier's "Config" menu item "Firmware EEPROM configuration" screen. Enter the correct values for both X and Y calibration, and then click on Save to EEPROM. Verify yes, you want these values in EEPROM.
Finally, make sure that your Slic3r configuration does NOT have any M92 commands which would override these nice, clean values. If you use Slic3r from within Repetier this can be tricky because you have to control which configuration file for Slicer is being used by Repetier by its name alone.
<Soapbox> I wish that Slic3r gave you clear visibility of much, much longer names for the configuration files it creates. When you have dozens of options to choose when storing the configuration file, it's impossible to give clear and meaningful names that fit inside the tiny selection windows they give you. </Soapbox>
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