Wow it has been forever since I last saw an fli/flc video let alone dealed with one.
You choice of codec/container aside it is a simple thing to resolve.
Some stuff appears upside down when you decode them using broken codecs (usually with directshowsource in avisynth: what batchdpg is doing), you have a couple of options:
add flipvertical() somewhere in the AVIsynth script.
If you use FFDshow to decode on some level (enable decoding raw video if you have to) you can flip video on the output section.
If you use another codec it may have flip vertical options although I can not speak for that.
You could also add in intermediate stage and convert to something else, bunch of stuff for it:
http://woodshole.er.usgs.gov/operations/modeling/flc.html