Accurate short-term wind forecasts (STWFs), with time horizons from 0.5 to 6 hours, are essential for efficient integration of wind power to the electrical power grid. Physical models based on numerical weather predictions are currently not competitive, and research on machine learning approaches is ongoing. Two major challenges confronting these efforts are missing observations and weather-regime induced dependency shifts among wind variables at geographically distributed sites. In this paper we introduce approaches that address both of these challenges. We describe a new regime-aware approach to STWF that use auto-regressive hidden Markov models (AR-HMM), a subclass of conditional linear Gaussian (CLG) models. Although AR-HMMs are a natural representation for weather regimes, as with CLG models in general, exact inference is NP-hard when observations are missing (Lerner and Parr, 2001). Because of this high cost, we introduce a simple approximate inference method for AR-HMMs, which we believe has applications to other sequential and temporal problem domains that involve continuous variables. In an empirical evaluation on publicly available wind data from two geographically distinct regions, our approach makes significantly more accurate predictions than baseline models, and uncovers meteorologically relevant regimes.