The AEC files are imported, not opened. If they don't import, then 9 times out of ten you installed the wrong import plug-in version. Definitely double-check that. Other than that I can only think of wrong settings being used in C4D, but we'd need much more info to unriddle that...
From the R12 Exchange Plugins folder I have CS3/CS4 and CS5 as my options for the plugin (obviously I grabbed the CS3/CS4 version since I'm still running CS4), placed it in my AE > Plugins Folder. From my C4D Render Settings > Compositing Project File I've got Save, Relative, and Include 3D Data all checked with the Target App set for AE. There's nothing abnormal going on with my C4D animation; its just simple geometry (a Television - hoping to add video content to the screen in AE - TV's screen has an external compositing tag) with 2 lights and an animated camera. Unless I'm seriously overlooking something, the .aec should work, but AE wont respond in any way. Its frustrating me to no end!
My Finder window says that my C4D.plugin is a Adobe Soundbooth Plugin...that cant be right can it? I've never noticed that before. ...but never had issues before either...