The file is a new one but it's based off of another file that's been used in the past. Basically just opened the old file, made changes to it and saved it out as a new file.
The only plugin I'm using at the moment is the Extensis Auto-Activation plugin.
When I save the file I use an customized version of the "Press Quality" pdf preset with crops, bleeds, and Illustrator editing capabilities enabled.
I have not tried rebuilding my prefs yet.