Whenever i try to sync using rio emplode or either Jemplode it gets to checking disk media and stays there forever, after maybe an hour or two it will finish doing that and sync.

How can i fix this?

The fsck (file system check) probably errors out for some reason (how big drives?) A manual stepthrough of the fsck procedure from the command line is called for...

General procedure, sheck/follow the links as well...

Potentially misleading initial FAQ link for a newbie. He doesn't need to rebuild his databases, he's getting "Checking Media" which is a different thing (although a messed up filesystem might cause database screwup, he still needs to fix the filesystem first).

The proper launching-point FAQ entry is here.