Q: Every single time I open iTunes, I have to manually add this UpperFilter in order to activate iTunes successfully.

There is not a published solution on the internet that I have found to resolve this issue yet.  I never had this issue until I upgraded to iTunes 11, so this is an issue unique to the iTunes 11 upgrade.  iTunes 10 would not have this issue:  

When I open iTunes, I get this error message:  "Warning! The registry settings used by the iTunes drivers for importing and burning CDs and DVDs are missing. This can happen as a result of installing other CD burning software. Please reinstall iTunes."

The following article manually resolves the issue:  http://support.apple.com/kb/ts3299

This article suggests I need to add an UpperFilter to a specific registry.

When I add th UpperFilter, open iTunes, it opens with not problem.

However, when I reboot, my CD-drive is no longer recognized by my PC. 

So, I research to determine how to make my CD-drive work again.

The resolution to the issue is to go to the specified registry, identified in this article, and DELETE the UpperFilter.

Uninstall the CD-drive from My Computer.

Reboot.

The CD-drive re-installs itself, and now works. 

Then, when I open iTunes, I get the error message again: "Warning! The registry settings used by the iTunes drivers for importing and burning CDs and DVDs are missing. This can happen as a result of installing other CD burning software. Please reinstall iTunes"

So the ONLY manual workaround I have is to do the following: 

While the computer is on, check this registry and make sure the UpperFilter is NOT in it.

Reboot the computer.

CD-drive works fine.  I can play a CD.  etc.

BEFORE opening iTunes, go to registry and ADD the UpperFilter back.

Open iTunes. 

iTunes works, and my CD-drive works.

DELETE UpperFilter so it won't force me to uninstall my CD-drive and reinstall it on an additional reboot.

Note:  I did review the following article that attempts to address the issue of the unrecognized CD-drive:  http://support.apple.com/kb/TS2308

I looked for additional drivers and I have the most up-to-date drivers installed.  This is an Apple issue, not a CD-drive issue. 

It also suggests to uninstall, and reinstall iTunes.  I have over 20 gigabytes of manually burned CDs I don't want to lose.  I am a little afraid of uninstalling iTunes as it might make my 200 CDs disappear from my hard-drive. 

Any help would be appreciated.  At least, in the long run, I do have a manual work-around. But this is truly lame that I have to do this to get both to work. 

I would like to transition away from iTunes and use a non-Apple product. Any suggestions would be appreciated.