I don't know in which tool you're seeing this, but I see nothing of the sort in DLTCEP. I see one sequence with two frames (0 and 1). I'm not even sure it's possible to have frames with the same number in the same sequence.Um, “cefc1inv.BAM” has one sequence (Sequence 0) in which there are four frames (Frame 0, Frame 0, Frame 1, Frame 1).
You can remedy this somewhat by smoothing or anti-aliasing the edge with the background colour (brown or whatever it is). I've never seen any loss when converting 256-colour bitmaps to BAMs, but maybe that's just me. Might have something to do with following the advice here if you're using BAM Workshop.BAMs can be less jaggy, but without alpha channel blending, you get the jaggy effect at the edges, where it's noticed most.