After flashing minimum gapps over standard gapps, it seems that all strange behaviors are now gone. No more delays when turning the nexus on (was up to 5s sometimes! ) no more system freezes either. I am running cm11 4.4.4, but this may apply to other roms as well. You can find it at http://www.androidfilehost.com/?fid=23501681358554723
I wiped cache and dalvik after flashing.