Methods for automatically programming a signal generator in a patient therapy system and associated systems are disclosed. A representative method comprises retrieving data including therapy program parameters, level of efficacy, and medication use corresponding to a plurality of time periods identifying from the data a target time period having a corresponding level of efficacy determining from the data if medication was used during the target time period determining from the data if medication was used during a prior time period immediately before the target time period calculating a lead position confidence factor and programming the signal generator to repeat therapy with the therapy program parameters corresponding to the target time period if the confidence factor is greater than a threshold value and medication was used during the prior time period and not during the target time period.
