Works fine here... even with different size clips selected:
(scaling together both SD and 720 clips up to a 1080 Timeline,
and scaling together both 1080 and 720 clips down to an SD Timeline).
CS6.0.3 / pc
Try selecting every clip in the Timeline, right-click
then select 'Scale To Frame Size'.
The effect will be null (no change) on clips that already match
the scale of the Timeline, then you can go through any problem clips
and check that 'Scale To Frame Size' is in fact selected.
You might have some letterboxed material in your
Timeline that will still have black top and bottom
even when 'Scale To Frame Size' is applied.
Also, any 4x3 clips in a 16x9 Timeline will have black
left and right when using 'Scale To Frame Size'.
For any oddball clips, use Motion Effect > Scale
instead of applying 'Scale To Frame Size'.