Hi,
What system are you using to comm with the Sabretooth, if it is serial, what port are you using?
If it is the Serial port rather than Serial1 or 2, the Mega is programmed through Serial, so connecting the USB will put data on that Serial and corrupt the Sabretooth data stream.
A complete schematic will be preferable as we can then see if you have bypass caps etc.
Use a pen(cil) and paper, it can be quicker, please label components and pin name.
Thanks.. Tom.. 
