You could try doing a null conversion from bam to bam with samtools:

samtools view -h repA2.bam | samtools -bS -o repA2-new.bam -
mv repA2.bam repA2-old.bam
mv repA2-new.bam repA2.bam

In theory this should result in an identical file, but maybe it will smooth out whatever anomaly is tripping up cuffdiff. But I'm surprised that cufflinks accepts the file but cuffdiff doesn't. I believe they use the same code for reading BAM files. Mayeb you should double-check that your cufflinks and cuffdiff commands are from the same version of the Cufflinks distribution.