Scribbler noticed this and posted it here: viewtopic.php?f=32&t=8675#p73053
I can verify that having file names such as:
O.Level.pdf
IV.RNA.pdf
and the like will not work in Scrivener. The file could be imported, but it cannot be used.
Edit: Scribbler takes credit for this find. The significance of the issue merits its own thread, and probably sooner so people can circumvent the problem while a bug-fix is underway.