Partition Table Looks Different Between OSX and Windows 7

Question

Hey all,
I recently replaced the hard drive on my 2007 iMac, going from the 320GB drive to a 1 TB drive. It actually worked! The previous drive was failing in very odd ways, though booting into the Windows side (more on dual boot later) always seemed to work, and S.M.A.R.T. always reported that the physical drive seemed OK.
The previous drive (320 GB) had around 200GB devoted to OSX and 100GB partitioned off for a working Windows 7 installation (custom installed x64 Win7 Ultimate). I had the Windows system image backed up to my NAS, and had a Windows system bootable disc to restore that image.
After replacing the drive (and almost crying that I had actually done it right), I first restored OSX from a Time Machine backup, and let it take the full 1TB of space as Journalled HFS+. Then, I used Disk Utility to shrink OSX down to 500GB, and created a second partition (formatted to NTFS) with the remaining 500GB.
Now, restoring a Windows system image is an odd thing, as it tries to do a lot of partition work as opposed to simply restoring the Windows install to a partition. I tried Macrium Reflect first (made a backup in that, too), and it looked like it was going to let me restore to the second partition. It completed the restore...and the entire hard drive was hosed. Partitions had been moved, renamed, resized, and nothing was bootable. I had to use Recovery from an external USB thumb drive to go back to the single, full-drive install of OSX.
Then I tried again. Made the second NTFS partition and used the basic Windows System Restore disk to restore from the standard system image I had on the NAS. I was not expecting this to work. But it did. Windows started showing up in Startup Manager when "option" was pressed on bootup, and both OSX and Windows booted properly and ran fine. This is where I (finally) get to the supreme oddities:
OSX Disk Utility still reports two 500GB partitions, one for OSX and one for Windows.
In OSX the Windows partition shows as having NO DATA on it. Not sure what would happen if I tried to write a file to it when mounted, but there is no data on it when viewed from OSX (I was always able to see the Windows files when I mounted that partition on the previous drive).
The Windows partition does not show up as a valid bootable system in System Prefs --> Startup Disk (naturally, I suppose, since OSX doesn't think there is anything there).
From the WINDOWS side, Windows still sees the old partition table: 200GB for the "unknown" HFS partition, and then the rest of the space can be devoted to Windows (started as 100GB, but I was ablt to expand it to use the remaining ~750GB!).  Windows thinks it can have 750GB of space even though I know its partition is only 500GB in size!
Windows cannot see the OSX HFS partition data using HFSExplorer. It CAN see the HFS partition on the attached backup drive (the drive I use for Time Machine).
GParted (a partition program on a Linux bootabld CD-ROM) shows the same partitions as OSX Disk Utility (2x500GB), and also thinks the Windows NTFS partition is empty (all space reports as "unused").
Did I mention both OSX and Windows work fine???
There are, of course, two other partitions on the drive: the first partition is the 200MB one I always see (EFI/GUID portion?), and then between the HFS and NTFS partitions is the 600MB recovery partition (which also shows at option-pressed boot time). OSX, GParted, and Windows see all four partitions, and in the same order. It is just that Windows sees the wrong sizes, and OSX cannot see any data in the Windows partition.
Surely this is all going to break spectacularly at some point, isn't it? What if I ever did write a file to the Windows side from OSX, or what if OSX starts taking more space than the 200GB Windows thinks is the max for that partition? What if I try to make Windows use more than 500GB because it thinks it has almost 800GB to use? What if I defrag the Windows drive?
I had no idea a partition table could look this goofy and yet still have everything be bootable and workable. Is there something I can do to get everything in sync? Basically, I am assuming I need to get Windows to do some low-level kung fu in Disk Manager in order to properly get everything lined up with the "right" partitions as reported by both GParted and OSX Disk Utility. But how do I do that?
By the way, any ideas that totally nuke the drive and start from scratch are completely fine (if it seems like they are doing something different enough that I'd give it a try). I have good backups of both OSX and Windows and have restored them about a half dozen times already as I dealt with the previous failing hard drive and with trying to get dual-boot working again. Not to mention, this iMac is now my secondary machine to the new Mac Mini I got a couple weeks back when I wasn't sure how much more life I was going to get from this 6+ year old iMac.
Thanks for listening to me ramble about this very odd issue, and a huge THANK YOU in advance to anyone who has ideas to help.
Thanks,
sutekh138

Answer 1

Update:
I am pretty sure the issue is a simple GPT/MBR discrepancy.
I installed rEFIt and used it's partitioning tool (gptsync built in) upon bootup. It was able to show the GPT table and the MBR table, but it thinks the second partition of the drive (the Mac OSX bootable partition) is "extended" in the MBR table and says "will not touch this disk."
However, it does look like an MBR sync should be straightforward, as there four partitions in the GPT table and four in the MBR (and MBR allows a max of four, AFAIK). I just need gptsync to relax some rules. I found a link to a supposedly newer version of gptsync compiled for OSX, so I will try that later.
First, I will try Partition Wizard, a free tool I found for the Windows side. It has a "Repair MBR" option that I would have tried last night if I weren't running a new Windows Image Backup in case all of this goes haywire.  *smile*  The PW tool also has an option to change the MBR over to GPT entirely. That might work, but then I am not sure Windows 7 will boot (from what I read, x64 Win7 running on EFI-enabled hardware should work, but who knows).
Anyway, I will try the following things, in order, until something works, when I get home tonight:
From Windows, run Partition Wizard and try "Repair MBR".
From OSX, download recent gptsync and try to run it.
From Windows, use Partition Wizard to do a full MBR --> GPT conversion.
Nuke the Windows partition in OSX Disk Utility, expand the HFS partition to take up the whole drive, and then add a Windows-bootable partition via Boot Camp-ish command line commands (diskutil). Because if nothing else works, I have to assume I just created the partitions wrong in the first place such that a Windows restore miraculously works, but the partition weirdness is just a timebomb waiting to happen.
Finally, if none of the above work, I'll just get things back to the way they now work and wait for the timebomb to (possibly never) go off.  *smile*
I'll update this thread if I get something figured out, in case anyone else stumbles upon it...
Thanks,
sutekh138