Prusa i2 z axis slow

long story short - new guy, built i2, had issues with no motor movement, tracked to 5v supply and not 12.
Now my X and Y move great, extruder works great, z-axis is sloooowwwwwwww. almost like 1mm of travel for 10mm requested.
Using Repetier Firmware 0.92 (config.h attached) and Repetier Host
I have a TOM running, but cant sort this prusa movement.
I have M8 threaded rod, so I think the steps/mm should be 2560 (per [nathan7.eu])
The travel speed is 2, so it should move kinda slow, but I think it should be a bit faster, and definatly further.
Nema 17's, on a RAMPS 1.4.
I have tried a few different settings but nothing seems to make the z move faster/further.
My EEPROM setting in the config is 1, so I think it will flash, but I have edited the sketch and uploaded successfully multiple times, but no perceivable change.
I plugged the X axis into the Z port, and fired a 10mm change, and while not as speedy, it moved 10mm. I dont think it should have.
The x axis is belt driven, so I would think it should be a different result.

I am not sure what I am doing wrong at this point, and my google-fu has come up wanting.

thanks in advance for your time.

EDIT: A4988 driver Pololu step stick

Edited 1 time(s). Last edit at 02/15/2016 05:11PM by spurgco.

Well, seems I just needed a break from the whole thing.
I went through Repetier again, and looked into the EEPROM flag on the setup.
It says:
"If you enable eeprom, you can change the most important parameter after installation over the host. Please be aware that the eeprom values overwrite settings in Configuration.h! To overwrite exiting settings select a different eeprom set. "
So I started thinking, maybe it isnt overwriting the settings, which would explain why the X axis moved the same distance because I defaulted the whole first time and the Steps/mm would have been 80.
Set the EEPROM flag to EEPROM2 and uploaded the new config.h
Z Axis moves the way I would anticipate.
Sooo, what exactly is the EEPROM flag doing?