There is an important bug in the 0.5.0 version it looks like when you use the batch with the manual mode or auto,user format mode, the program always works in automatic mode.
This leads to images having different formats and possibly wrong extensions.
This problem occurs only when using batch.
I will solve this problem in the following days. Meanwhile you could switch to latest stable – 0.4.6 if you want to use the batch mode with manual settings.