For sure MadMapper send the same signal to the HDMI than if you have no HDMI->SDI converter below.
I suppose you have an SDI connection issue that triggers depending on the input signal. To "debug" the issue, I would suggest putting MadMapper in a state where the SDI signal is lost at projector, take Syphon Record (and publish MadMapper projector to syphon) so you get a perfect movie of MM fullscreen output. Now you can send the same signal as MadMapper from QuickTime player. You should get the same issue. If that's the case, you know you don't have to look in MM to find out.