Emma pretty much covered it...you really do want all your dots to line up, and since they start on the right and space evenly toward the left, the varying length of the text on the left determines the space before the first dot.
You can put the cursor between the word and the first dot and use tracking to either add or remove a dot. Sometimes you can get it to look a little more consistent than Quark does automatically.
Only semi-related to the actual question: I usually use a period then a space for the fill characters. Sometimes there are just too many dots, and fewer dots can give you a cleaner look. Depending on the font, this might also make those problem spaces less obvious.