Magatsu1 is pretty close to the answer. The problem isn't the size of the polygons but the number of sides they have. If you have a poly with more than 20 vertices most of the converters fall over and stick their legs in the air.
Cutting the polygons in half using the polygon draw tool splits the poly into two new polys with half the number of edges.
Have a look through my FAQ for the ship creation guide. IP Andrews covered most of the serious problems that can cause problems for a ship in FS2. Of course some of these are now redundant if you're building a ship for HT&L since that automatically triangulates a ship on loading and therefore won't suffer from the vertices in a line/non flat polys problems that other versions do.
