Incase anybody else comes across weird height resolutions when encoding with specific parameters, setting the profile to auto and then manipulating the level and other parameters put the height back to 1080 with very high bitrates.
We tried to reproduce the scenario, resulting in wrong height for you, but could not. Did you modify the SDK 2012 encoder filter in any way that may cause this?
That said, for the case when using the SetParams interface to set profile or level etc., the sample code will ignore any specific parameter settings and instead use the parameters implied by the selected preset. If you want to override any of the presets just remove the last code line "CodecPreset::VParamsFromPreset..." from the function CopyEncoderToMFXParams in "mfx_video_enc_filter_utils.cpp".