Cramtools Lossless Compression

I've been using Cramtools to compress bam files but I'm not getting the results I was hoping for.

If I try lossless compression

java -jar cramtools.jar cram -I file.bam -O file.cram -R genome.fa --capture-all-tags --lossless-quality-score

It will convert the file to cram. Although when I decompress the bam file it changes dramatically. The reads are changed but not the quality scores. The decompressed bam file is typically smaller than the original, even with the addition to the header. If I compress and decompress this file afterwards it will not change at all the way it did the first time.

Can someone please explain to me how to use cramtools properly? or is this the expected output?