I hads an acer notebook awhile back. Seems they forgot to remove a plastic cover between the vent and the styrofoam spacer; this piece completely covered and blocked the vent, although I couldn't tell until I had dismantled it (it was transparent plastic). Given my history with them, I'd probably dismantle it first to make sure that they didn't leave these vents covered up before firing a brand new machine up :/
Also, did you make sure you cleaned off the old compound before adding new stuff? If you don't get a nice even / flat surface covering, then it will create gaps and not provide adequate cooling.