you need to make sure that dual extrusion is selected and that you have got the temperatures set for both extruders - also make sure you've got them selected properly on the setup page for the printbed.
Don't think I've had any heating issues with makerware. but you do have to double check every thing.
If you change the print speeds - it will reset everything else, so any time you change the speed settings you have to go back and reset all the other settings.

It's my biggest gripe with it. Well that and not being able to change basic settings for a custom profile without editing the whole bloody thing.