So I wanted to try the new Android Studio and imported my eclipse projects (I generated a gradle build file). Worked pretty good.
The only library which does not see
I had the same issues, followed the instructions for configuring aa with intelliJ, now it works like a charm does.
AA intelliJ config page will point you to this post...
http://www.ashokgelal.com/2012/12/setting-up-intellij-idea-12-with-maven-actionbarsherlock-roboelectric-androidannotations/
...the above post walks you through setting up various libs in intelliJ, scroll towards the bottom for AA.
The main thing I had to do that I did not have to do in eclipse was go to Preferences > Compiler > Annotation Processors and set my Processor Path to something like...
[PATH TO AA JARS]/androidannotations-2.7.jar:[PATH TO AA JARS]/androidannotations-api-2.7.jar:[PATH TO AA JARS]/codemodel-2.4.1.jar