Folder with question mark keeps coming back

Hello there , i have a problem with my mac pro.
The problem is that every time i start up the mac it can't find my startup disk and then gives me the Folder with ? mark in it.
Some times just do a start up for the second time helps but most of the time i will have to hold the alt button pressed, and then some times i get to choose my start up disk from there but most of the time it then starts up from my boot disk.
When it has started up and i then go to the pref's , select my boot disk and lock the prefs so basicly it would not be able to chance that disk without my password, i find the next time i start it up, with all the same problems, the lock is also no more activated in my prefs.
I tried several things already, resseting power management, pram , Applejack, combo update 10.5.5, repare permissions ...., until now nothing helped solve the problem.
My Mac Pro 8 core, was just back from the dealer to get a new raid card battery and it worked fine for a while.
The startup disk is disk 1 in JBOD on the raid card by the way.
I feel that this problem started occuring after the 10.5.5 and java updates
but since those 3 things came very close together i'm not 100% sure.
I hope someone here can help me out with finding a fix for this problem because i have run out of ideas and i wanna avoid a reinstall of my system .
Thank you for your help ,Data from the Netherlands.

I tried several things already, resseting power management, pram , Applejack, combo update 10.5.5, repare permissions ...., until now nothing helped solve the problem.
I am not ready to say Applejack is as safe as it use to be.
I can say that making a backup with SuperDuper is essential; as is having OS X "EMergency" boot partition or drive (FW, someone said that used 8 or 16GB SDHC memory card).
And use Disk Warrior along with Apple First Aid to repair your drives.
Anytime you zap pram or SMC you have to reset the startup disk, and it sounds like your disk or NVRAM is a problem.
Personally, I like a single fast dedicated boot drive; or, a stripped RAID (and instead of mirror better off keeping a good backup image cloned).
So clone your system only to another drive with SuperDuper.
Repair your boot drive with Disk Utility and Disk Warrior (or TechTool Deluxe/Pro).
If you think 10.5.5 may have caused it, roll back to 10.5.4, that is what backups and making a clone of your boot drive are good for. And always make a backup before you even begin to upgrade the system.

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