i dont like to store my bottles laying down...is that paranoia or can the bottle cap actually impart bad flavors in the beer after a while
This. Cap/cork "taste" is one issue, though opinions will vary. A bigger issue has to do with bottle conditioned beers and the need for the yeast to be as settled as possible prior to pouring. Upright storage ensures that it will happen and that decanting, if you so choose, will be easier.
I do both due to the way my beer/wine fridge is set up. My try to do more vertical for the same reasons mentioned above. That said, I haven't had any issues with the one's stored on their side. Just had a BCBS that was on it's side for 10 months and noticed zero difference from one's that were stored vertical.
I laid a Tart of Darkness on it's side to age for a little, but a special occasion came up only 3-4 months after, and when I opened the cap the stuff they line the bottom of the caps with was eaten away and the beer had a very strong metallic taste, so yes, corks and caps can cause off flavors in beer, store them upright!