I think you're misunderstanding something. There is no (and never was a) Zotero plugin for acrobat or any pdf reader. Where did you get that idea?
I'm not quite clear what you expect those plugins to do? Pdf files are indexed when you store them with Zotero - it doesn't matter how you open them.
http://www.zotero.org/support/reporting_bugs
P.S I have already installed the two plugins for indexing pdf files and this works ok when I'm indexing pdfs whithin firefox.
I'm not quite clear what you expect those plugins to do? Pdf files are indexed when you store them with Zotero - it doesn't matter how you open them.