Did there used to be more options when importing a file in Bookends? It gives me a choice between Bookends, Bookends Pro, Bookends tab-delimited, and XML (EndNote).
None of them worked with the text file I exported from JSTOR (under the option "Directly export citations into EndNote, ProCite, or Reference Manager.") I used to be able to import the file without a problem, but I'm not sure what changed, maybe it used to be a .ris file. If I try XML, I get an XML parser error.
Sounds like Bookends can't find your Import Filters folder. There should be two (one required): Import Filters, in the same folder as Bookends, and Custom Import Filters in ~/Library/Application Support/Bookends.
I have the Import Filters folder in the Bookends Folder under Apps, and it has JSTOR in there. My custom import folder is empty, but I don't think I had anything in there.
I did delete my prefs recently, I was getting some error when trying to launch. Can you tell if there's anything I need to do?