If there is one thing that is annoying when you us pdflatex in Emacs, it is the behavior of Adobe or another commercial product. If you haven’t closed the pdf-file, Emacs or better LaTeX will complain that the pdf-file is still open. I found some tricks in the internet, but I did not manage to implement them properly (you can for example use sumatrapdf, but I wanted to keep my original pdfreader on my computer).
Finally, I decided to use my macro/script program winautomation (www.winautomation.com). I bought this program a few months ago after getting tired of the open