[Doom9]

And are you 200% sure that once you press the autoencode button, you set the radio button to No Target Size (use profile settings) and that in the profile, the mode is set to ABR, Const. Quality or Const. Quantizer?
Especially the former is important.. you never confirmed that you're doing this. My 1P-Intermediate is set to ABR (so downloaded by the autoupdater).. but you MUST change that radio button or all will be for nothing. Unless you set the radio button to that particular setting, the number of passes configured in the settings will be taken.. and since the minimum there is 2 passes, you'll get two passes irrespective of the profile. I've tried this about 10 times now and the result is always the same..