Yes, there is a ext2 limitation with respect to samba. I believe ext2 can't handle files over 2gb in size.
In past versions of Samba, I've noticed that samba didn't do a good job or reporting file sizes on windows shares but never as bad as what you're seeing. I'm fairly confident that there's nothing with SME that's causing this.
I'd suggest posting to the samba mailing list. If you don't want to subscribe, I can post a question for you. Let me know.
Greg