growing different varieties of chillies

i want to grow different varieties of chillies this year.  My answer is will cross pollination affect the fruit grown from each variety.  Last year i tried growing several varieties and got odd yellow chillies with no flavour, some scotch bonnet and what i thought was dorset naga's, which looked the part but were very mild taste. 
I grow in a greenhouse.  any suggestion appreciated as i don't want the same thing to happen this year.

thanks
puffinstuff