I'm using AUCTeX with emacs 24.1 on Ubuntu 11.10. I have the TeX Command set to compile using LuaTeX and to produce pdfs. Everything works except that the name of the pdf changes from the file name to textput.pdf. Not a super big deal but the same thing happens with the index and I have to rename it to the file name in order to get the document to compile with an index (defeating somewhat the purpose of the convenience of having the Index command available in AUCTeX).
I've seen reports of this issue elsewhere on the internet but not being very knowledgeable about the inner workings of emacs I have been unable to figure out how to fix this behavior. I had been compiling everything with XeLaTeX and it all worked as expected with respect to the resulting file names, so this appears to be a problem with LuaTeX or how AUCTeX deals with LuaTeX.