Flashing ? on Dual-Boot MacPro

I'm having an intermittent issue on a large number of our Mac Pro's. We have 96 Dual Boot Mac Pro's we use in a lab environment. When booting up some of these machines they hang at a grey screen (prior to the apple logo) for about 5 minutes. Then they eventually display a flashing question mark. To get around this issue we have been holding the option key and choosing the desired OS. This works as a temporary fix, but it's not a good long term solution.
Our Dual-Boot Setup is as follows: Dual Hard Drive
- HDD1 has 3 partitions
• Macintosh HD (Mac OS X Student Partition)
• Boot Partition (My Mac OS X Admin Partition)
• System Drive (Windows XP Student Partition)
- HDD2 has 2 partitions
• Student Drive Mac (HFS+ Data Drive)
• Student Drive PC (NTFS+ Data Drive)
40 boot automatically to Windows XP
56 boot automatically to Mac OS X
Resetting the startup disk in System Preferences seems to fix the issue temporarily, but never permanently. I haven't been able to diagnose specific machines having this issue more then others. They are all the same spec and same software build (imaged with ASR and WinClone).
Anyone out there have a solution?

none standard partitions. Having XP and more than one other user volume. There are a GPT and one or more hidden EFI (200MB and 128MB) also. So there are 5 or more partitions instead of just 4 that Windows Master Boot Record can handle, and it is last one.
I don't like having Windows and Mac OS on same drive.
Having data partitions on #2 drive is something I would always do.
My guess is that the Mac partition was original just one, and was then divided or shrunk to make for a 2nd partition which is causing trouble. Same thing happens if you shrink Windows partition to then have, say, XP and Vista or something.
Using 3 or 4 drives would make it all work easily, and WD Caviar 500GB $49 each or better are my first thought (just bought Black series and it is not as fast as 640GB model but still good).
Shame it can't be don't in VM and with hardware virtualization.
- just rebooted my Mac Pro to Windows 7 and it is about 45-60 seconds, or about the same as either of the PCs sitting here also running 7 RC - from on to desktop.

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    The large print: please read the Community Participation Rules before posting. Include as much information as possible: model, machine type, operating system, and a descriptive subject line. Do not include personal information: serial number, telephone number, email address, etc.  The fine print: I do not work for, nor do I speak for Lenovo. Unsolicited private messages will be ignored. ... GeezBlog
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    HI Manish_5
    "Is it possible to role back to my previous Windows 7 in future" but you have to create now the backup (recovery disk) to later use:
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    Rollback:
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