Hi,
I haven't used boolean software in a few years, I primarily use solidworks now, so I may not be too helpful but I remember running into problems with infill if the boolean union had scrambled geometry due to crazy curves. I also just started using meshmaker for creating my own custom support for my prints, and I noticed that the program is used primarily for making boolean meshes. its free you should check it out if the problem persists. Sorry I'm not more helpful, figured I should toss out a few ideas.