OK, at this point I believe I may have lost you or at least we are not talking apples to apples. The problem plain and simple is I no longer have write access to the root folder of the secondary partition. Before the re-install, it worked fine. I re-installed Windows 7 on the PRIMARY partition only, and left the secondary partition alone, yet for some reason now I have no write access to the root folder of the SECONDARY partition from anywhere on my laptop, go figure.
I try to manually create a folder in the root folder from either the primary OR secondary partition - "Access Denied". I try to create a folder in another folder anywhere on my laptop (which I can still do), and then copy it to the root folder on the secondary partition - "Access Denied". I attempt to change Security on that folder from either the primary or secondary partition and the options are grayed out. The secondary partition's root folder seems to be totally write protected, and I don't know why?
Where you may have gotten confused is where I asked about installing to the primary partition's root folder (I have complete access to it) and copying to the secondary partition. This question was probably amiss anyway in that I couldn't copy the folder to the root folder of the secondary partition anyway. I would have to try to run it from the secondary partition when booted to it, and attempt to create needed registry entries - well this is a bad idea no matter how I look at it.
The whole problem is that I need access to the root folder of the secondary partition which seems to have become write-protected after I re-installed Windows 7 on the primary partition.