Plugin installs and activates but does not work

I have several domains running wordpress 2.8. Some of the installs have been done manually using the official WP package and some other installs I have used Dreamhost’s one-click install function. So here is the weirdness: on the installs with “Dreamhost one-click” plugins such as shadowbox js. and google analytics install and function perfectly. On my other manual installs of WP, the same plugins install and say everything is fine, but there is no settings dialogue that comes with the plugins and the plugins aren’t activating on the page. I’m pulling my hair out over this I’ve installed reinstalled, re-downloaded wp source files, changed themes. And yes I have checked to see if the plugins are compatible with 2.8. Everything works perfectly on “one-click” installs using exact same setup, theme, plugins. etc..
Anyone else have experience with this madness??