I have the same problem. I have linked to three different manuals (php.net, local HTML and local CHM). None of them work with shift+f2 or "Open PHP Manual". I really miss the manual integration I used to enjoy in my previous IDE It isn't a deal breaker, quite, but I think it is a serious enough problem to deserve attention.
what version are you guys running?
im on win7 eclipse 3.6sr2 / pdt 3 shift-f2 works fine for me.
if i click on then hover a php function, it gives me the tool tip with the man page in it
hitting shift-f2 then opens the php web page in firefox