It appears to be doing it over and over again though. It use to auto organize and only do it once.

Auto-Organize Files will overwrite a file with the same name and it highlights these in red in the Auto-Organize Files window.

I'm having issues where it does add a number sometimes but it overwrites my library entry instead of just changing my library entry. I had to shut down auto scan and continuous scan. I also shut down auto organize. It was re adding songs already in my library.

I guess you're referring to Auto-Organize instead of Auto-Organize Files as Auto-Organize Files overwrites instead of appending a number.

I've noticed this many times, when files have the same value for the fields used to auto-organize the files then they conflict and the files are automatically renamed with a "(#)" at the end of the file name. This is all fine, but the algorithm for choosing which number is with which file is non-deterministic so upon scanning the files are always renamed or copied unnecessarily and I constantly end up with duplicates or lag because of this. Could you not base the number at the end of the filename on the modified date of the file or it's hash or something?