[texhax] equations number backwards

[Max Lein]

I've encountered a very strange bug in my PhD thesis: equations at one point start numbering backwards, e. g. equation (B3) follows (B3), then (B1) and the next is (B-5). The number of decrement seems to correspond to the number of lines that do not have an equation number (I'm using the align environment and I would set the \notag flag in the lines that I do not want numbered). 

There is no suspicious output in the log file. 

I'm at a loss here since I have never encountered this phenomenon before. So far, I've done the following: 
- I've tried using pdflatex instead of xelatex (no effect). 
- I've deactivated hyperref (since there were some `pdfTeX warning (ext4): destination with the same identifier' warnings), but no effect. 
- I've tried using book instead of scrbook as documentclass (no effect). 

There is nothing special about the code I've used. I can post some sample code, but the whole document is ~200 pages long and split into quite a few tex files. In fact, I've used part of the code before in papers without any problems. 

Can anyone point me in the right direction? I've tried googling it, but came up empty. If you need anything, please let me know. 

Thanks. 

Max