The performance of GaN-on-Silicon electronic devices is severely degraded by the presence of a parasitic conduction pathway at the nitride-substrate interface which contributes to switching losses and lower breakdown voltages. The physical nature of such a parasitic channel and its properties are however, not well understood. We report on a pronounced thickness dependence of the parasitic channel formation at AlN/Si interfaces due to increased surface acceptor densities at the interface in silicon. The origin of these surface acceptors is analyzed using secondary ion mass spectroscopy measurements and traced to thermal acceptor formation due to Si-O-N complexes. Low-temperature (5K) magneto-resistance (MR) data reveals a transition from positive to negative MR with increasing AlN film thickness indicating the presence of an inversion layer of electrons which also contributes to parasitic channel formation but whose contribution is secondary at room temperatures.