ok it looks like you have the right extruder as T0 and the left as T1. now look at your controller board on the printer and see how you have the extruders hooked up. i bet you have left extruder hooked to the T0 output and right to T1
I'm talking about in the printing process setup window. (Don't have the software here. I can check later) There is a tab where you can have g-code scripts that run when a before a print starts, ends, at layer change, etc. The line usually looks like:
T0 ;select the right extruder
It usually also has code to home the print head, do a purge, etc.
If you had started modifying a process that was originally for the wrong extruder, that line shown above would still be there even though you changed the extruder for layers and support.
What printer do you have? Are you sure you have the firmware settings in the software setup correctly? For example, if you have a Replicator 2X, you need to go to Tools -> Firmware Configuration and choose the MakerBot/Sailfish firmware profile. Then click on the X3G tab and select the Rep2X. If you don't follow those instructions, it won't print with the correct extruder.
Yeah same idea. I think the Wanhao D4 is just a clone of the Rep 1 dual. Follow the instructions above, but in your case I think you would select the "Replicator 1 - Dual Extruder" on the X3G tab.
They made things really easy for your since they already include profiles for the Rep1's. You should be able to choose what extruder is used by picking the between the "Replicator 1 Dual (right extruder)" or "Replicator 1 Dual (left extruder)" FFF profiles.