New Melzi 2.0 setup on i3, Strange results from MatterControl

I recently upgraded my i3 to a real Melzi 2.0.
After much hair pulling I finally found the magical combination of Arduino IDE 1.0.6, sanguino harware files that work
& whatever version of Marlin I had used before that not only got MatterControl to connect but also let me select my thermistors specifically. (Other didn't seem to offer that option).
All seemed relatively well until I started exploring the control responses today. Something is wrong and I'm at a loss for what.

Sometimes giving movement commands works and sometimes it doesn't.
I can pre-heat the hotend and bed BUT, when I tried to tell MatterControl to start printing, the bed and hot end didn't start heating at all.
I have the motors rolling in the correct direction but it seems that telling them to 'home' not only moves them AWAY from their endstops but also makes the print declare that the axis is now moved to it's maximum, even though it hasn't.
Also, clicking 'home' will get the machine to move the axis a little bit and then stop, even though it thinks it is in home position.

I think that's everything but I may have forgotten something. I saw enough weirdness out of it...
The Marlin I'm running is, I'm pretty sure, the same settings I was using on the previous Melzi board, a '1.5'.

Help?
I'm so confused right now...

Still need some help but I've worked some things out.

I'm focusing on getting just the X axis completely straightened out.
It's moving in the correct physical direction now. Homing X is moving in the correct direction as well. HOWEVER...

When I tell an any axis to home it moves only a little bit and then tells the UI system (Matter Control) that it has moved to it's maximum distance.
So clicking the 'home' button results in the printer thinking that all axis' are now moved to their maximum positions... which is nuts because I have Marlin set for minumum endstops, not max.
It's rather confusing...

Oh, probably unrelated but, I seem to be unable to save EEPROM settings.

Fixed the problem with homing setting the location to maximum.

Two remaining problems.

Homing is going in the wrong direction, physically.
Viewing the machine from the front, clicking X- in MatterControl results in a movement of the head from right to left, that is, towardy from the endstop, as it should be.
Clicking the home button for X or all axis moves the head AWAY from the end stop... huh?
The position readout however, shows a reduction in position by the correct amount, again as it should.

It's almost like the endstop needs to physically be on the other side, but even that wouldn't be right.

I've looked through MatterControl and can't find a setting in configuration.h that would have the necessary effect, except for setting the endstop as MAX, but that would then have the position reading saying that it moved in the positive direction.

Help?
Anyone?

plug the stepper motor plug the other way round to reverse the motor direction.