When to try 'Repair' to a Win 7 upgrade from Vista?

Have Desktop with Win7 32 upgrade from Vista (not clean install). Laptop came with Win7 64. Have new Transcend 500GB ext hdd. Immediately recognized on laptop, and readily installed included software pack on it. Connect to Desktop it is recognized, but the software pack on the ext hdd will not function. Problem posted on Hardware forum. One response from MVP suggested that the problem might be from the upgrade without clean install, as those were not always perfect. All other properties of the drive checked out fine, such as drivers, no yellow triangles, etc.

Is it possible that a repair might now solve this problem, or that the upcoming(?) SP1 might take care of such? If so I'd want to clarify the correct procedure for the repair. Did SFC this morning and it found some problems and corrected them, but my problem still persists. Suggestions appreciated.

I'll be doing the clean install as you both suggested. Will there be any problems as I will be putting 7 on top of 7? Will formatting be done once it is established that I am entitled to do so?

Thanks for the very quick response! I'm lucky to have my laptop next to me that has everything on it that the Desktop has. Good for reference and fall-back. Now I just hope that this solves the problem with the ext. hdd, as I really want to use the software pack that came with it.

And, after the reinstall the Transcend ext. hdd. now works as it should, thanks to zigzag who first raised the question about the upgrade installation being faulty and you two suggesting the method of solving the rest of the problem.

Nice to know, thanks.

Be sure to check optional Updates for newer drivers, too.