We examine the current response of molecularly controlled semiconductor devices to the presence of weakly interacting analytes. We evaluate the response of two types of devices, a silicon oxide coated silicon device and a GaAs/AlGaAs device both coated with aliphatic chains and exposed to same set of analytes. By comparing the device electrical response with contact potential difference and surface photovoltage measurements, we show that there are two mechanisms that may affect the underlying substrate namely, formation of layers with a net dipolar moment and molecular interaction with surface states. We find that where the Si device response is mostly correlated to the analyte dipole, the GaAs device response is mostly correlated to interaction with surface states. Existence of a silicon oxide layer, whether native on the Si or deliberately grown on the GaAs, eliminates analyte interaction with the surface states.