Okay, I did some reverse engineering and what I found out was:
1. The print bed center of the CTC has the coordinates X0 and Y0. This must be set in in the settings.
2. In the Start GCode, when homing the axis (G28), they didn't get calibrated. This must be done using G92 X152 Y75 Z0 A0 B0. If this isn't done, the printer doesn't know where it is, that was the reason why prints were off-centered.
3. When using the Sleep function, the printer goes to X-115 Y-75 Z150. If (default by Mattercontrol), the coordinates X0 and Y0 are the front left of the print bed, it tries to go below these values, resulting in hammering.
My Start GCode now looks like this:
G28 ; home all axes
G92 X152 Y75 Z0 A0 B0
G0 Z5 F5000 ;set warming position
M1200 MatterControl; Build Start Notification for Makerbot
When using Makerware, there is an A and B axis for the two extruders. I will try to find out how this effects Dual Printing.
Would be cool if you could add this as a new printer profile!