Winlogin is deleting folders and files on start-up

We have been using Crystal Reports Server X1 Release 2 since 2007.  Week ago folders started dissaperaing and found out that there was a conflict with McCaffe update that deleted business objects folder and Tomcat stopped working.  Now we are trying to restore VM from prior file deletion and everytime we boot that up winlogin seems to be applying settings and deleting folders again.  Help!!!

Not to insult ... this is presented as it is to be sure all facts are given ...
There are two levels to disk formatting:
Disk-level
Partition-level
Disk-level, which defines how "partitions" are organized.  There are two disk-level formats you need to be aware of for Mac:
MBR (Master Boot Record), which is used by Windows systems.  This is the one you most likely have on your existing disk.
GUID is used by Mac.
Your MBR disk can be left at MBR, in my opinion.  It is likely at least 2 years old, and any backup disks you buy for Mac-backups should be new, in my opinion.
Within a disk, there are "partitions", with different formats:
Windows uses a method called NTFS.  It has in the past used FAT, FAT32, but both are replaced by NTFS for most systems now.
Mac uses HFS+
Microsoft has a patent on NTFS and only grudgingly allows other computers to even read the disks.  Technically anyone could red it, but Microsoft may at anytime pull the plug and sue any "entity" or operating that tries to read it.
My suggestion is this:
Buy new disks for backing up your new Mac system.  Make them self-powered, already formated for Mac.  Buy new snice backups need to be on reliable hardware.
Also buy new disks for keeping "files only" directories for your new "mac-world".
Use your old disk to move files off as needed, but it is now a "secondary" disk used to read old files.

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