Borders will have no reason to make elements behave like blocks.
I'm assuming that what you mean is when you apply borders it drops the next div down? When you add borders it adds to the total width of an element.
Say you have 2 columns, both floated and the parent is 800px wide.
You set them both to 400px and then you set one column to have border:1px solid red;.
That's 2px total borders and thus the width of both columns = 802px. Thus since it doesn't have room to fit it will drop dwon thus a float drop.
Count your widths on the columns, borders/margins/paddings add to the total width of the element. Make sure they all match up and there is enough room :).
If not you can post a link to the page in question and we will sort this out for you
Firebug is a great tool for debugging.