About 10 years ago, a study was conducted to see if they could isolate the brindle gene, find out where on the chromosome it was located, and if they could determine the genetic mechanism by which its expression is regulated. It was an interesting study and worth reading the results if you are into that kind of thing.
More fascinating is that during the course of gathering and analyzing DNA from Boxers in the UK and Europe, they found a dog that was phenotypically (appearance) fawn but genetically brindle. That dog's great-grandfather was a well-known brindle that had NEVER thrown a fawn pup even when bred (pretty prolifically) with fawn females and so had been determined to be heterozygous brindle. He had been statistically proven to not even have the genes necessary to produce a fawn pup, yet he did! It was hypothesized that a specific genetic mutation had occurred and been passed down the line.
This just goes to show that even with strict breeding programs run by people who know what they are doing, nature can still shake things up. When it comes to genetics, no matter how much we think we can control, it's still just a crapshoot.
All Boxers are really fawns. Brindles just have another gene that gives them their stripes on the fawn base. In turn there are other genes that tell the brindle gene where and how much to "turn on" which is why you see some really dark, heavily "stripey" brindles and some not so much. Genetics, and especially the heritability of genes that determine the degree to which other genes are expressed, is not always straightforward. When you have a number of genes all acting on each other, if even one small mutation occurs, you can wind up with some really weird outcomes.
This probably doesn't help you a whole lot in determining how you register her though. The bad news is that she might never do well in the conformation ring. If she is indeed a brindle, she's not brindle enough to show and if she's a fawn then she's likely going to be faulted in the ring for her spot. It looks to me like you might be in a lose-lose situation.
Now, if you are registering her so you can compete in AKC sanctioned events that are NOT conformation (agility, obedience, rally, etc.) then I would just register her as a fawn and be done with it. Her spot might make people say "hmm?" but it won't affect her trialing career.
If your heart is set on showing, I'd ask a bunch of breeders and even some judges opinions on the matter. They'll be able to tell you what to do and if it's worth your time showing. If she isn't a show quality pup and it was represented to you that you were buying a show quality pup, you may be able to return her for another pup or get a partial refund on your money. It all depends on the terms of your contract.
