HT201366 The second hard driver (internal) was disappeared in my MacPro, after this update.

I found an error message, "the second hard disk was ejected", when my MacPro was resrarted after this security update 2013-003 .
The HD was diappreared in the system.  I cannot find it in finder, disk utility, and terminal. 
The other problem I just found is that some applications working with Java are not working.
Any suggestions or advice would be greatly appreciated.

Updated the video card firmware
Sounds odd.
A more complete list of hardware of course helps.
Every new OS puts more stress on hardware resources and can turn up what worked but marginally so.
I see a lot of threads with OWC FBDIMMs showing half their capacity for one or two DIMMs.
They also can run too hot. Hence using SmcFancontrol 2.2.
Monitor things with Temperature Monitor
And I always reformat hard drives when it is time for a new OS.
Backup and clone the sytem first, or leave as is and opportunity for a new hard drive.
Then test it out and only later import and migrate.
The Mac Pro often needs boost the fans slightly and can suffer from dust (X1900 especially).
8800GTs have always been known to fail.
You may have 7300GT? those are old in the tooth.
If OS X 10.5 was running off an Apple RAID, the RAID needs to be created with 10.6 or it won't function and install properly. But you don't have RAID or didn't mention one.
Most often 3rd party drivers.
Avoiding eliminating Kernel panics
FAQ kernelpanic
Resolving Kernel Panics

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