Hey Stephen,
Thanks so much for getting back to me. I did eventually figure out how to log the installation of the 2 products.
I've been trying to figure out what's been going on, and basically, this is what I can gather.
I released Product A with the two shared files in a merge module, and the components were both being installed to:
C:/Program Files/Common Files/My Company/My Product/Share Files /file.exe
C:/Program Files/Common Files/My Company/My Product/Share Files /file.dll
Product B and C used to be separate, and Product B used to contain the same merge module as Product A. It became unneccessary for Product B and C to be separate, and so I combined them into Product C, by basically adding to Product C all of the merge modules that used to exist in Product B. When I did that, I noticed that none of the newly added merge modules from Product B were installing the correct location, so I rebuilt all of them. And they then installed to the proper location.
The problem is that when I rebuilt the merge module that is shared with Product A, I fixed the path of the files for the merge module to:
C:/Program Files/Common Files/My Company/My Product/Shared Files/file.exe
C:/Program Files/Common Files/My Company/My Product/Shared Files/file.dll
Note that I corrected the path and removed the unneccessary space after Shared Files. However, I did NOT change the component GUID.

And I believe that is where my problem comes from. I also did NOT rebuild the product A installer with the new merge module!!! I know...I know...stupid.
So now, Product A installs the files with Shared Files /, and Product C installs the files with Shared Files/ (no space). And since they have the same component GUID, the ref counts are messed up, which is why when I uninstall Product A, it removes files in use by Product C.
Basically, HKEY_LOCAL_COMPUTER/Software/Microsoft/Windows/CurrentVersion/SharedDLLs looks like this:
C:/Program Files/Common Files/My Company/My Product/Shared Files /file.exe(1)
C:/Program Files/Common Files/My Company/My Product/Shared Files /file.dll (1)
C:/Program Files/Common Files/My Company/My Product/Shared Files/file.exe (2)
C:/Program Files/Common Files/My Company/My Product/Shared Files/file.exe (2)
Because Shared Files /file.exe and Shared Files/file.exe have the same component GUID, when I uninstall, I assume that it's checking the first instance of the comp GUID, and see the reg count as 1, and just uninstalls the files.

The log file is like Russian to me, but I was able to discern from it that the installers had the same component GUIDs.
So long story short, I get that I f'ed up, but now I just need to come up with a plan of action to fix it.
And to confuse matters even more, on our website, we have a link to download Product A and Product C installers separately. If I install Product A and Product C individually, instead of installing Product A as a PRQ to Product C, the reg counts are fine and there is no incorrect Shared Files / path!?!?!?! And the product code, package code, everything is the same. It's installing the same exact installers, but when it installs as a downloaded PRQ is the only time I see the incorrect path and ref counts.
Note also, that even when there are ref counts under the Shared Files / path, there is no actual folder installed to the computer named Shared Files /. It is installing the files to Shared Files/.
So I've tried renaming the component GUID, and then fixing the path, but that didn't work to remove the incorrect reg counts. I've tried RemoveRegistry, but haven't really been able to see that it's working. I must have it wrong somehow.
Even if I do a major upgrade, it does not uninstall the Shared Files / entries from the reg count, and it's set to do a complete uninstall before installing the major upgrade.
Thanks for any advice any one can give!!!
~Bilandra:)