When I copied and pasted the code from http://www.zotero.org/support/kb/exporting_from_endnote_with_pdfs into a notepad document, saved it and tried to run it, I immediately got this error:

Windows Script Host:

Script: C:\...\ris-fix.vbs
Line: 9
Char: 1
Error: ActiveX component can't create object: 'UserAccounts.CommonDialog'
Code: 800A01AD
Source: Microsoft VBScript runtime error

I'm on Windows 7, 32 bit, if that has anything to do with it.

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I gave up on that and decided to replace it manually, but I had some issues using Find & Replace because my EndNote export had something like this for each reference:

L1 - internal-pdf://Beard & Johnson (1999) - Iron Isotope Biosignatures-1347130891/Beard & Johnson (1999) - Iron Isotope Biosignatures.pdf

I'm not sure why it had that extra subdirectory thing going on, or if it's like that for everyone (doesn't seem so), but I thought I would share the solution I found for fixing the internal-pdf:// issue in the RIS text file exported by EndNote.

Using the standard "find and replace" function in Notepad++ (this doesn't work in Notepad, not sure if it would work Wordpad), search for:

internal-pdf://*.*/

and replace with:

file://C:\Users\me\My Ebooks\

That selects everything up to the first slash after the ones in internal-pdf://, allowing you to insert file:// directly in front of the appropriate path.

I then saved the text file and was able to import the library and the attached PDFs into Zotero. The URL field for each file was populated with file://C:\Users\me\My Ebooks\[filename].pdf, but only if it had been blank before, it seems (otherwise it retained the URL that had been there in EndNote). And the references that had had attached PDF links in EndNote now each have the appropriate PDF attached in Zotero, appearing as FullText.pdf.

I'd only call it a partial success since I wish I could just import a LINK to the PDF rather than have an attached, read-only duplicate of the PDF, but that's another post :)