Terminal Server not respecting one association in HKEY_CLASSES_ROOT

I am running the Terminal Services role on Windows Server 2003. Yesterday, all users started experiencing a problem where double-clicking a PDF file opens it with the NTFS short name (8.3 format), so if any changes are made, the file is saved under a different name.

I have already used ASSOC and FTYPE to ensure that the system-wide file type associations are correct.

ASSOC .pdf=AcroExch.Document
FTYPE AcroExch.Document="C:\Program Files\Adobe\Reader 9.0\Reader\AcroRd32.exe" "%1"

I used regedit to confirm that the contents of the respective registry keys (below) matched the parameters given to ASSOC and FTYPE (they did).

HKLM\Software\Classes\.pdf
HKLM\Software\Classes\AcroExch.Document

However, Windows seems to disregard these settings completely when opening a PDF. Note that using "Open With" works correctly and opens the file with its long name, despite being configured with exactly the same string. In fact, I can delete the shell/open/command key entirely without having any effect. When the user double-clicks a file, it still opens with the same program despite no longer being specified in the registry.

Even stranger is that under Folder Options / File Types, the entry for PDF File says that:

You have customized files with the extension 'PDF'. To restore these files to their default type (Acrobat PDF Document), click Restore.

However, there are no per-user customizations for this file type. I inspected HKCU\Software\Classes and there are no entries related to either PDF or Acrobat.

This problem persists between logouts. The only workaround I've found is to log off, delete the user profile, then log back in to create a new profile based on the default user. Then the user inherits the system-wide settings as expected.

My next troubleshooting step is to restart the server, but I won't be able to do that for several hours yet. Has anybody ever seen a problem like this before?