The shape of the bottle will probably change conditioning if theres more contact between teh yeast and the beer, and possibly speed up carbonation. From what I've read head retention (neglecting anything artificial that reduces is) is based on the viscosity of the beer, which can be increased by long-chain, unfermented sugars, dextrins, etc. so different bottles shouldnt technically change head retention.
Do you bulk prime? If not, you may have some inconsistent carbonation. It could seem like there is better head retention when in fact its just more head.
Could also be something to do with how you pour from the bottle, and as mentioned possible embossing on the inside of the bottles. Once again, this could increase head, but not theoretically increase head retention.