I have the same issue. It's been happening a lot lately. So I started experimenting with different files last night. Saved the longest to the night so it didn't hinder my progress on actual translations. What happened is that I woke up today to find it still aligning (no error or frozen screen, it was just taking its time, or that's what it seemed to be doing). I ended up aborting the process. Then, I tried with another PDF of the same file, but much, much shorter (actually the overview). It's been aligning since this morning. This is the first version that makes me struggle so much just to align a couple of files. 

Clearly something isn't right and if you're aligning a PDF that would be the best place to start investigating.  I suggest you convert the PDF to a DOCX before you align it and clean it up to remove unnecessary tags, ensure the para breaks are correct etc.

PDFs are never a good way to work... even if we do say we support them.  There are PDF files and there are PDF files... but there is no consistency.

Clearly something isn't right and if you're aligning a PDF that would be the best place to start investigating.  I suggest you convert the PDF to a DOCX before you align it and clean it up to remove unnecessary tags, ensure the para breaks are correct etc.

PDFs are never a good way to work... even if we do say we support them.  There are PDF files and there are PDF files... but there is no consistency.

That's indeed a very good idea. I'll convert, try again, and let you know how it worked out. Thanks for the prompt response! 

Tried. Didn't work. I can provide screenshots. It's been processing the converted (Word) docs for about 2 hours now. 

Can you share your problem files so I can test?  You can send them to pfilkin@sdl.com if this is ok.