I'll second that.I haven't noticed that, but in my opinion, Spotlight is not the best search tool to be using. There are other alternatives that do a much better job than Spotlight.
Here's one you can try: Find Any File.app $7.99 in the Mac App Store.
It's not that it can't find PDF files -- it can -- it's just that it often can't find the ones I know are on my iMac's hard drive.Spotlight is more than capable to locate .pdf files.
I assume that Spotlight's index needs to be rebuild.
You can use a maintenance tool called ONYX to do that.
( I have never had any issues with Spotlight and PDF file, I use Spotlight every day ) Cheers ... McBie