Plasmid sequencing failed why? - (Jun/28/2011 )
It's very hard to know what is happening without a lot more detail and some experimentation. The sequencing primer site could be missing from your "correct" clone which shows the RE digest pattern you expect. The sequencer could then be sequencing some other plasmid contaminant present in your sample (or carryover from the ligation). I'd re-transform your DNA, streak for single colonies, miniprep and try again. You could also try some additional primers sequencing from your insert into the plasmid.
You might be better off making the construct again and throwing these away.