If the MOBI is always DRM-free, then
Calibre is better than mobigen at ePub to MOBI fomat shifting. With the 0.6 version you will also be able to convert to many other formats. If you get an error with mobigen your only realistic option is to change the input ePub to work around it, with Calibre you can report the bug and get is fixed quickly. I don't know how good Calibre's command line error reporting is though.