i have had the same problem. but finally found a solution.
this is in the PermisssionsEx permissions like, btw.
i added a new user group like so;
Craft:
prefix: '&0(&8craft&0)&7 '
permissions:
- modifyworld.*
- essentials.*
options:
rank: '892'
inheritance:
- Member
then added the fake users like so;
BuildCraft:
group:
- Craft
IndustrialCraft:
group:
- Craft
RedPower:
group:
- Craft
ComputerCraft:
group:
- Craft
ComputerCraft Turtle 0:
group:
- Craft
ComputerCraft Turtle 1:
group:
- Craft