This is an old thread, but I still have this problem on my kindle today, so I thought I would post this solution.
No need to mess around re-saving with compatibility. Just put in the correct metadata (agree with the suggestion of using Last, First to get good author sort) and re-name your file. I just put an extra space at the end of the filename before the dot - ie
"File Name.pdf" becomes "File Name .pdf" I guess when Kindle detects a filename it never saw before, it gets the metadata fresh.