After importing the scene in C6 just conform the clothes again to the character and zero it (the button below conforming). For some reason conforming is sometimes lost or not completely applied.
Do not panic if a piece of clothing suddenly changes as you conform another piece of clothing, just select the misbehaving piece and conform again. In the end everything will look right.
Poke through can be corrected by taking the piece of clothing into the editor and gently pulling the appropriate vertex (with soft selection). Just pull a bit and go back to posing to check the result.