Alright, so i had a working wordpress installation hosted at GoDaddy, i moved it to my own VPS, following the wordpress guide. Which seemed to work, after some problems with .htaccess. (Moved by copying the entire wordpress directory and updating the SQL database details in wp-config.php)
Then i updated wordpress manually which was completed successfully, then the problems started. First new blog posts produced a blank white page, i troubleshooted this and found it was one of my plugins doing it. Next problem is uploading media (pictures, others untested) upload as corrupted. When i say corrupted, i'm not sure if they are, navigating to a image URL throws a wordpress page not found and they are shown as blank images in the media library.
Moving from GoDaddy to a VPS is obviously going to mean the paths of the actual wordpress install has changed, is there anywhere that needs updating? (/var/www/wpblog).
Permissions as far as i know are untouched.