Have you tried launching the new Adobe Reader 6 application once yet? Launch it directly from the start menu.

I did the same thing you did - upgraded Acrobat Reader 5 to the new Adobe Reader 6. All of the sudden, all of my .pdf files lost their association to the reader application. I found that launching Adobe Reader a first time completes the installation process. After this final step, everything fell back into place.

What tipped me off is that after I thought the installation process was complete, and I tried to double-click any .pdf...when the "choose program to use" dialogue box appeared, there was no Adobe Reader or Acrobat Reader listed as an available application.

Give this a try, and see if it helps you. Good luck.