Bill, this is really late in the coming, but you'll notice W7 constantly complains "X may not have been installed correctly...select to reinstall with recommended settings" I have found these notices to be completely erroneous in all cases. Furthermore, it irritates me that it only gives you this warning after you install your 4GB program...
I am guessing, but I think that most of all, it is to warn you to set an appropriate compatibility mode for the installer. After all, if you select "reinstall with the recommended settings" after that warning pops-up, it just re-runs the installer in the appropriate compatibility mode. If you don't the setup (and the resulting program) may not function properly; in my case, all of my apps were fine without it.
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Dell Latitude D630

Win7 x64 Pro