Any reason not to use PDF's?
If it flips, the solution is invalid. If planes do not align, the solution is invalid. Need I go on? In short: You are expecting too much from this simplistic tool. It just can't deal with these things and your overlapping, blurry grids are a clear indication of that.
Thanks Visheh for the link, I will cehck it out.
Mylenium: I don't get all of your message, that says that if there's an error that's because the tool can't do it. I've seen lots of examples done with the phothoshop>vanishing point>after effects process that really look perfect and way more complicated than the ones I did for tests (in which some are okay regarding the blurry grids, or the planes alignment and some are not). So I guess there's a trick somewhere that I'm missing, I can't just blame the tool, because some people use it and get good results.
EDIT: Visheh, the tutorial is good somehow incomplete (as ever). Check this one too that can help also (wish this guy did a lot more, I like his way of teaching)