Render Sequence via Panel is slower?

Hi, I created a panel that renders the active sequence with Adobe Media Encoder.

We tested it for a week now and video-editors say that encoding via panel is slower than when they do the same task (Encode sequence in Media Encoder with exactly the same preset and target path) manually.

I told them that this is not possible, because both tasks do exactly the same. Is that correct?

Are there any settings / configuration options for  app.encoder that may impact render performance?

Thanks