You are 100% right on this one. It was a problem in sketchup. Between the bottom layer and the bottom layer of the "compartments" was set to a gap of 1.5mm. I increased the gap to 1.55mm, exported again and bam it works, no more weird shapes. Also tried going shorter to 1mm and it worked normally again. I can't understand for the life of me why it's upset with 1.5 but hey.
As for my problem with no infill. I've narrowed that down to version 5.0 of cura. Like I said I went back to version 4.13.0 and then infill works.
What version of cura do you use? Also thank you for your help, I appreciate it!
I added the fixed version if anyone wants.
CE3PRO_Box V2.1.obj