in one of our projects we created a site collection template by createing the onet.xml file and so on
and we configured the template to activate some features when ever trying to create a new instance of that tempalte..

but some of the features were using some web.config keys of the webapplication that the new site collection is beeing added to..

and amazingly we find out that when ever creating new site collection when it tries to activate the features it uses the web.config of the central administration site instead