Ah, I don't think the auto texture can actually handle that type of shape. Basically they work very differently to any of the other elements. Try removing those shapes (the ones you have to make with co-ordinates) and see if the auto texture will run. You may have to replace and set their texture manually.
Or if your model isn't a stupid amount of parts you can try doing the offsets by hand. It takes time to do but you can actually save yourself some time when it comes to making the texture (e.g. if you have two parts that need to be textured the same you can simply assign them the same texture offset rather than giving them two different positions).
Stephen King wrote: “Don't ask me silly questions
I won't play silly games
I'm just a simple choo choo train
And I'll always be the same"
If you're using MC 1.7.10 or an earlier version and you want to keep the shapes, try cloning them and deleting the original ones, so they're left to end of the list of parts that TB will map. This way, all boxes are mapped normally and you can map the shapes manually afterwards.
If you're using MC 1.8, just replace the shapes with shapeboxes. Shapes aren't rendered properly in the latest Flan's Mod version so there's no point in going through the previous process.