We have seen the odd unusual case where Vista/W7 setup can write boot data to *three* separate partitions, one of being the boot drive, the second being the system drive, the third being by accident.
What you are experiencing may be some variation of that scenario, in which case you will need a specific solution for your machine.
I would try fixing it with the D: offline, and assuming that your W7 is not booting properly despite appearances. Ignore "if it ain't broken don't fix it", just this ONCE
With the D: offline, try using the boot repair options on the W7 DVD -- or alternatively use VistaBootPRO to force installation of the Vista/W7 boot manager on all drives. One trick I have to clear an old Vista boot menu and replace with a clean one, is to use VBP to install the Legacy boot drive and then *immediately* without rebooting reinstall the Vista/W7 one.
But try the W7 DVD first, and make sure you reboot a few times before putting the D: back online
Of course you may be right and it could be a bad registry entry -- if no other fix works, then just reinstall W7 with the D: offline (...)
Hmmmm I do have one question : have you defined the root of the D: drive as the Documents folder or have you mounted the drive into a system folder ?