The only thing I can think of, if Windows Disk Management gives different results than your software, is to compare the MBR Disk Signature between a drive done by WDM and one done by your software. What are they setting?
My general situtation is that I have 2x SSD Data Drives & an SSD Boot Drive
The MBR Signature my software is producing are of the format:
00DFC325 - Data 1
005ECD34 - Data 2
00000001(Boot/OS Drive - OCZ Turbo SSD)
Ones that I have seen from Windows Disk Management:
123096F4 - Data 1
153096F6 - Data 2
A3023969 - Data 1
A302396B - Data 2
9EBF9RBF(Boot/OS Drive - Intel X25-E SSD)
D895AE4B- Data 1
D895AE49 - Data 2
DD57DD57(Boot/OS Drive - Intel X25-E SSD)
The major issue that I am having is that when I boot up with drives that I have initialised in my software the boot order will be changed to use them rather than my OS drive. When I use Data disks initialized with Windows Disk Management I do not have this issue.
Well, clearly the Boot/OS drive data is quite different. I can't tell what role the BIOS would be playing here, though.
I would almost suggest asking for help from people who also code their own drive initialization/formatting software, maybe. It's pretty far beyond the scope of the normal server stuff we see in here.