The problem doesn't happen to often. I'd say once in every ten backups. And yes its not database specific since if I get a faulty backup (contains BOM) if I immediately repeat the process I'll get a dump without BOM. One additional information which might be of use is that I've noticed this behavior since the last two-three patches. It wasn't an issue before that.
dfForge 6.1.154
MySQL 5.5.35 (CentOS 6.5)

