Link some logs and I'm sure people will be able to find any problems much easier. Use Simcraft to give yourself an idea of the dps you are potentially able to do, though.
Just to add to this Simcraft is not perfect not just because of bugs as such, but because how rotations are written in the system at least the default ones.
For example, as a Affliction lock myself and lot of people report doing more DPS on average than simcraft results.
Simcraft is only good for stat weight are figuring the base of rotation (most of the times).