At some point, I think fairly recently, something got messed up in the background tests of the ENMTools R package and it is building the models for the permutation tests using incorrect presence points. I think I've found the issue and am working on a fix right now, but if you're using a recent version from CRAN or GitHub to do background tests I would not trust those results until a fix gets released. I will do my damnedest to get that done this afternoon, Japan time. Really sorry for any inconvenience this might have caused.
edit: I think I've got a fix for this on the develop branch on GitHub. I'll work on merging it into the main branch and then prepare a CRAN release.