File systems, do they matter, huh and what happened to my data?

[spazzy]

I have two external hard drives which I sync together with SD. The source drive (HD1) is formatted with mac os extended (Case-sensitive, Journaled) the destination drive(HD2) is formatted with mac os extended ( Journaled).

I synced today between the two and right after accidentally blasted a bunch of stuff from my source(HD1). I used smart copy to sync my source(HD1) to my destination(HD2) but I noticed two strange things

1) my source drive(HD1) has 10G extra data than it should which really confused me so I sync HD1-->HD2 but still HD1 has more data (number of files and drive space used)
2) A bunch of random files are missing from both the HD1 and HD2 drives


what gives?
I can only guess this is because the file systems are slightly different?
Each time I sync it was with smart copy.