Alright so I seemed to have answered my own question from my previous post.
I had first used NCS to program my gf's e90 battery so when I went to use NCS on my car I thought I could just remove all the files in the work folder and leave a .MAN file. When I did that I also removed the other file CABD which was one of the error messages I got when I hit Process Car at the end.
Luckily I didn't erase those previous files, I just moved that one and a .fr file back from my trash.
I went to try coding this morning using the recommended NCS Dummy and voila! It worked! At first I thought it hadn't because the NCS window said it wasn't responding and it never said coding ended but I turned my car off then on and Lord behold it worked.

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"Hey, Now that's what I'm talkin' about, Jack!"

Current:
2002 X5 3.0i E53 - Max

Previous:
2003 XB9s - Rebeka(missed)
1993 525i E34 - Elizabeth(sold at 83K miles)