I have uploaded version 1.01. The only changes are two new command line options: -batch combines /encode and /exit (added to be compatible with CCE 2.66 retail) and -nocancel hides the Cancel button in the encode progress dialog. Also command line options can now be indicated by either hyphen or slash.
I should also mention that right now custom 3:2 pulldown settings are not saved/loaded to/from the ECL, just the check state of the 3:2 Pulldown checkbox. Maybe I'll add support for the 3:2 pulldown settings in a later version if there is demand for it.
Oh, and in case you wondered: yes, it does load/save the VBR Bias setting from/to the ECL and applies it even if no VAF file exists yet