If you have a problem with larger videos not uploading and converting and you have checked all the other common settings that cause this then another thing to check is your servers apache httpd "timeout" value. You can sometimes see this in your phpinfo.php under "Timeouts: connection".

Mine was set to 30, so converting larger files that took more than 30 seconds stopped. I set this to 600 and its fine now :)

Just thought i would share in case someone has the same problem.