For starters, check which version of Slic3r you are running. If you have one of the older.910b-ish versions that shipped with many printers, try upgrading to the 1.0.0RC3 version. That fixes a specific bug relating to thin walls around round holes and thin infil sections not being fully filled.
Aside from that you could also try setting the “make complete layers ever X layers” setting more frequent.