I had a simular problem..
I was using the knoppix-remaster script to do the job.
It worked well for me, but dispite removing packages my Iso refused to shrink.

The problem was.. I had mounted another Partition to copy my custom scripts and files.
I never umounted the partition and the remasterd iso included the contents of the "other" partition.

Once I remembered to umount the un-need partitions my iso file behaved as it should.