I have never heard of this issue. Installing Adobe Reader will automatically associate all PDF (and other) files with Reader. I cannot imagine how they get associated with Notepad.
What is your Windows version?
What Adobe Reader version do you use?
How do you install them (from an EXE download, or an MSI download, other)?
This is something that I have been dealing with for years. I am loading version 9 on XP machines. For ease of installation, we saved AdbeRdr934_en_US.exe to our server and load from there. Usually, everything works fine at that point. It is only after I load the other apps to our system that I notice the problem. In any case, I can't just change it for me and expect it to be applied to all users. As an admin, I can change the file type association so that it uses the reader for pdf files. However, regular users are not admins and cannot make the changes. I don't know if one of the other apps (Enterprise Vault client, IBM3270, WinZip) that I load is messing with it or if the update is screwing it up.
You may want to try to change the installation sequence, i.e. installing Adobe Reader last.
I can rule out WinZip or the 3270 emulator as culprits, as I use them myself. But I don't know what the Enterprise Vault client; check if the associations have changed after you install that software.