If I remember correctly, Mecha Destroyer JD fixed it in one of his games by using HTML input instead. Can't remember for sure, so you'll have to ask him.
Yeh, we turned basically everything except the Chip Select Screen into HTML (Because the Chip Select Screen is one of the cosmetic favorites of BN Fans). Ironically that's one of the key crash points, although before that the key crash points happened to be whenever we utilized a weapon (which de-equips it from your equipped inventory), often freezing one or both players and freezing the turn gauge. It's hard to explain it without the reading party to know in detail how the BN Series works.
I don't know what it is, what HE is sure of is the fact we used a lot of images in it (I think it was transferred JPegs or Gifs, forgot which, it's been months since him and I Discussed it).
All I know is that it was going haywire since the first Alpha testing when two people actually began, however the more we 'debugged' the more 'bugged' it was. Before it would happen half-way through a "turn" and everything would freeze, the next thing we knew it happened whenever we pressed one of the built in macros to choose our Attacks in preparing for the first turn.
If you want, Kakashi will gladly send you the source (as he has stated) so you can personally review it, because this one's totally out of our hands.