Disappearing combo drive on 2007 mac mini in lion

I am having trouble with a disappearing DVD/cd-rw on a 2007 mac mini.  I purchased a used mini of ebay and upgraded to a SATA III SSD and 2 gigs of ram.  For the most part the system functions great.  However, the disc drive is not always recognized by the computer.  When its not recognized, i seem to get a kernel panic when i try to shut it down.
could this be a problem with the OS?  could one of the cables be loose?  I followed the iFixit guide for upgrading the ram and replacing the hard drive and had no problem.
I am also using an old Newer Technologies MiniStack with an external drive.  I did not power the drive on this morning and the combo drive was back and iTunes ripped a CD without issue.
Before i try another clean install, i would appreciate any insight you could share.

Could be a lose connection. I would try reseating the connectors

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