X264 Encoder missing one frame

[X5gb]

Encoding a finished Premiere project with 2 pass x264 either through Simple or Megui and whatever I've tried it is removing one frame at the twenty one second mark on the second pass (removing the final frame of the Paramount logo before it goes to black). Tried it with other encoders including Handbrake (not quite as good quality) and no such problem so am stumped as to what could be causing it. Have resorted to adding an extra black frame and see how that goes which I'm encoding at the moment but would prefer to work out what is causing this. First thought it might be a glitch in the source but tried it with a lesser second source I'm using in the project (from different original source) and surprisingly it does it with that as well which seems weird.

Any advice as to what could be causing this is much appreciated.