if your using the capper that i am, and i'm guessing you are, it's all a function of the first lip on the neck of the bottle. just so we're clear, the second lip as i'm referring to it is at the top of the bottle and is the lip to which the cap goes to. the style of capper i and again, probably you, are using uses this first lip to pull against as it applys the pressure to the cap and seals it. on a sam adams bottle there is a noticable distance between the two lips, on a bass bottle, there is significantly less distance. as a result the capper is essentially at the end of its travel when you reach the first lip on the bass bottle and hence the difficulty in getting a good seal. sam adams' bottles are no problem because the capper engages much more early in it's travel and hence you are able to get a proper seal with no added effort.
you can definitely seal on a bass bottle with the "crappy capper" but it may take a few tries. one important thing to remember is that even if you get the cap to form, check to see if it can twist, if it can you still don't have a good seal. once it is essentially locked in place and cannot be twisted then your seal is good, but don't crank on it to hard otherwise you may break what is actually a good seal.
final note, save your pennies like i am to buy a better capper so that this isn't an issue, like it was said above, many other bottles share this issue.