Don't know if this is EXACTLY the same issue, but I am seeing search issues in SharePoint. Have removed and reinstalled the PDF ifilters, removed and installed Reader 9 which contains the latest ifilters....no success.
Microsoft referred me to Adobe for a solution, but so far nothing.
I know this is a forgotten thread but I stumbled across it and wanted to point out that Version 9 of the Adobe Reader is busted. This relates more to Indexing Service on Windows 2003 Server but still applies as the description of problem is nearly identical.
Reader 9 is broken where talking to Microsoft Indexing Service is concerned. At first, I thought it was just a botched install of an update. After setting up a test server installing just Reader 9 and creating a catalog, I found the problem is not by chance.
I did find that the ifilter was not being properly registered with the Indexing Service in v9, but that fixing the registration problem didn't help.
Below is where to check in the registry:
Look at DLLsToRegister and make sure the AcroRdIF.dll is last in the list. The list is processed start to end so having the reader ifilter at the end ensures your pdf indexing won't get messed up by some other well meaning service.
Most likely, you won't find an entry in the list with the proper path information.
Adding the registration doesn't help with the v9 problems, but will help after reinstalling v8 and trying to figure out why it won't work either.
whole thing a joke