Why is Preview unable to search some pdfs that Adobe Reader has no problem searching?

In the last couple months, I've noticed that Preview is unable to search some (but not all) pdfs. These are clearly digitized journal articles, recently published. Since this didn't make sense to me, I opened the documents with Adobe Reader and found they were searchable using Adobe.
What is going on? I'd prefer to use Preview, since I'd always preferred its search function and like its annotation tools (specifically, the box outline tool I use to identify chunks of text). Should I just give up on Preview and switch to Adobe?

I can search that document in both Safari and Preview.
Back up all data.
In the Finder, select Go ▹ Go to Folder from the menu bar, or press the key combination shift-command-G. Copy the line of text below into the box that opens, and press return:
/Library/Internet Plug-ins
From the folder that opens, remove any items that have the letters “PDF” in the name. You may be prompted for your login password. Then quit and relaunch Safari, and test.
If you still have the issue, repeat with this line:
~/Library/Internet Plug-ins
If you don’t like the results of this procedure, restore the items from the backup you made before you started. Relaunch Safari again.

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Thanks. I knew that would work. But I am asking (I guess) why using control-click and choosing Preview doesn't. I notice that preview isn't included in Recommended Applications, but that is understandable given the suffix .cgi.
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Recently on my MacBook Air running Mountain Lion, Preview will not open some PDF's. Other PDF's it opens just fine.
Those PDF's that will not open in Preview display the following Adobe message in the Preview window:
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Why is Preview unable to search some pdfs that Adobe Reader has no problem searching?

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