If you use alot of code (like [color], [font] and especially weblinks), your sig can easily go over the "6 line" limit since long lines of text in the sig editor count as more than one line if they have to be 'wrapped' i.e. broken into two separate lines... so what looks like one line in a finished sig can take up two lines in the sig editor, which is probably what is causing you the problem here.
Remember that blank lines also count too...