folders/files disappear XP

I have been working on a laptop that seems to work fine except some folders disappear when the computer is shut down.  It is very specific in what disappears.  Any folder that alphabitically comes before the documents and settings folder will be gone after a reboot.  Doesn't matter if they have other files/folders in them or not.  I have also tried to hide files and about any other setting I could think of that might change things.  Files that come alphabitically after the documents and settings folders are not effected in any way and are always there.  Until recently we have been working around the problem by just naming every folder so that it comes alphabitically after the documents and settings folder.  Today though we needed to install a web based program and the program creates a folder and we can't change the name or the program will not find it.  The folder name starts with a "C" so it always disappears on restart.  
When the computer first boots a corrupt boot.ini error comes up for just a sec then the computer will go ahead and boot.  I have no idea if the boot.ini error is related or not.  The laptop is being used by a sheriffs department and came with software installed and we think the problem has been there from the very start.  All other laptops (same model and software installations) work just fine.

Other than just saying "that's odd" I'm pretty much lost.  Any ideas would be greatly appreciated.  I'm not even sure what zone to put this in.
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That sound as if it could be some behavior of malware. What anti-malware are you running?
Just to be safe, I would scan the pc. Try one of these. I personally recommend MSE.

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You can troubleshoot the system like this. First thing first, your first and important problem is boot.ini so the remedy is you have to run on command prompt SFC /Scannow with windows xp CD. If it does not help you then i would recommend you to restart your system and boot from CD now move on to recovery console and run a command bootcfg/rebuild it will rebuild your boot.ini file. When this issue resolve

Now  move on to your next issue which is file disappearing. This seems to be a spyware or some kind of virus so use a good anti virus and anti spyware like

Anti spyware (Use all of them but go with the numbering)
3.Himanpro surfright

Antivirus (Use any one of them)
1. Eset Nod32
2.Symentac endpoint
3.Norton ghost

Hope this will help you

Have you tried to create some test folders within Save mode and see if they still disappear? If they aren't disappearing in Save mode, then you can start a process of elimination by de-selecting startup items to see which one may be the culprit, if that be the case.
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Just to clarify my above comment, if you can get into Save mode to create a few test folders, the when you test to see if they get delete, you will need to reboot back into save mode to see if the file has been deleted.
could be a rootkit - try the AVG free remover :
kargen27Author Commented:
So far nothing I have tried will help with the missing boot.ini file.  I was able to create a boot.ini file but it disappears again when the computer is shut off.

I tried everything but Combofix from the list farjadarshad provided and found nothing but some tracking cookies.  I still have the problem with folders disappearing.  Still seems odd to me.  If I create two new folders and name one cfolder and another efolder the one named cfolder will be gone but the one named efolder will still be there.  

I haven't tried safe mode yet, that is next, probably tonight.  

They got this laptop at the same time they got six others, all exactly the same and with the same software installed.  None of the other laptops have this problem, but talking to the officer who has this computer the folders have been disappearing from the very start,  Until now though it wasn't a problem.  If they can find the software I'm thinking about just doing a complete reinstall.  Just in case they don't find the software though I am trying other things.
Thanks for all the suggestions so far.
did you try the rootkit?
kargen27Author Commented:
Quick update.  Tried the rootkit and all the things lee555j5 suggested. All they found was a few cookies that really were not any threat.  

As they have other laptops exactly like this one all with the same software would it be quicker to somehow just grab an image of another harddrive and transfer it over to this computer then put the personale settings back in place or would that be a major hassle?  
Still what really has me puzzled is how it only deletes folders that start with either A, B or C and everything else seems normal.  

 I did find out they provided me with the wrong disks for this computer so before I continue I am waiting for them to find the software that actually goes with this computer.  

that works only with an image from the same hardware
kargen27Author Commented:
Although the comments didn't help with this particular problem, the suggested programs have helped with other things that have since come up on other computers.  So I am splitting the points among those that shared resources with me I hadn't used before.

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Windows XP

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