The quickest way to extend a sequence is to use the convert to sequence option in song mode. Just set up a loop and the amount of repeats and hit convert to sequence. The new sequence will be the original sequence multiplied by the amount of repeats. I use that function all the time.
Like Artful said, it sounds like you're not setting the number of bars you want BEFORE recording your sequences. If you want 4 bars, but you already layed down a sequence with only 2...once you change the number of bars to 4 there's gonna be silence after the first 2 bars.