Maybe this is related to the fact the current online trial version works as expired, when invoked by the Windows search indexer, so not feeding the indexer with metadata. This happens because the search indexer works from a Windows user (system) limited account, so also the PDF-ShellTools property handler when invoked by it, making it fail to read the trial control data in this scenario (a new version is almost ready, with this problem with the trial version fixed). Even so, the files would not disappear, but rather pile in the unspecified group, or the trial expired message that is in this situation the metadata returned, and would show again if you arrange by a non PDF related metadata property. If this is not the case, I don't understand how the PDF-ShellTools property handler could have anything to do with this problem.
I suppose if you open the real folder, not the library one, the files are there and show the metadata correctly in the details pane?
By what property are you arranging by?
Acrobat Ifilter v9.0 64 bit installed. (this one is essential to make full text search work)
No idea if it may be the culprit, but probably not. But you can easily find out, disabling it temporarily.
And if you have your PDFs filled with meaningful metadata, you don't even need this, that only serves to slowdown, and eat resource from, your system. The property handler will also used by the search indexer to index the metadata properties, so the search functionality will continue to find your PDFs (obviously because of the problem I referred above it's not working with the trial version).