FileBot

I understand that Terra.Nova.S01E01.E02 is detected as Terra.Nova.S01E01
the strange thing, is that next file; Terra.Nova.S01E03 - is then deemed to be 02... and so on.

Please see attached screenshot.

Episode titles match perfectly. It's getting those correct with a good title, and falls back to matching by SxE for the episode "VS" (2-letter title match not good enough).

Your episodes names don't match what's in the DB so it can't work auto-magically. It'll need some manual intervention:
http://www.youtube.com/watch?v=OJca0ipOCAg

Here's TheTVDB data:
http://thetvdb.com/?tab=seasonall&id=164091&lid=7