Hi Jeff Schmied,
Since plain text files are indexing successfully, your core search engine is functioning normally. This narrows the problem down to either a permissions issue with the indexer or a failure with the specialized IFilter components responsible for extracting complex text from Office and PDF files. The Windows Search service operates exclusively under the local SYSTEM account context. Even if you have full administrative rights, if the SYSTEM account lacks explicit Read permissions on your file share folders, the indexer will only read the file properties and silently fail to parse the internal contents. Checking the NTFS security properties of your testing folder to verify the SYSTEM account is explicitly granted Read access should be your first troubleshooting step.
If the NTFS permissions are already correct, the registry mappings linking document extensions to their respective IFilters are likely corrupted. Reinstalling the Microsoft Filter Pack often fails to resolve this because Windows installers typically will not overwrite persistent registry keys if they contain existing, albeit corrupted, data. Since you have identical, functioning Server 2022 VMs, you can leverage them to easily fix the broken server without rebuilding it. Open the Registry Editor on a working server and navigate to HKEY_LOCAL_MACHINE\SOFTWARE\Classes. Locate the problematic extensions like .docx and .pdf, expand them to find the PersistentHandler subkey, export these specific keys, and merge them into your broken server to restore the proper Class ID strings.
Regarding PDF files, Windows Server often struggles with native PDF content indexing if a third-party PDF reader has altered the default handlers during installation or an update. You must verify the problematic server is running the exact same PDF software version as your working servers, as a mismatch can easily unregister the handler. After verifying the SYSTEM permissions and importing the correct PersistentHandler registry keys from your working environment, restart the Windows Search service, point it at your test folder, and rebuild the index.
Hope this answer brought you some useful information. If it did, please consider hitting "accept answer". Should you have any questions, feel free to leave a comment.
VP