Yup, that M107 must be it. It's the only difference between the two codes. Even if I put it at the very end of the start code it changes everything. No bed heating, slow homing...
So, a little clarification, at the risk of making myself look stupid. The info I had about the M190, M104, M109 codes was coming from the RepRap wiki g-code page. My memory told me it was 3D printer g-code in general. I guess there are still inconsistencies between the 3D printer manufacturers. In fact, the M107 fan off command is deprecated in RepRap; maybe that's the problem. I believe the FlashForge control is based on RepRap.
For now I am going to have to translate all my files through Replicatorg to clean out the M107, unless there is another way to get it out of there.
Unless, of course, I am still doing something wrong...
Still, nice piece of software! I've tried a few so far and this is my favorite.