I would suggest updating the LWJGL that minecraft uses to 2.9.0, a nightly build of LWJGL. It includes a fix for shift-clicking while having MC windowed and such.
link:
http://ci.newdawnsoftware.com/job/LWJGL-git-dist/lastSuccessfulBuild/
If that fails, try updating java and perhaps try installing optifine (you can google for both of those). If you still have problems after that, dunno what exactly should be done then.