If you are running PermissionsEX and it's accompanying ModifyWorld plugin, you need to make sure that [buildCraft] and [industrialCraft] have modify world permissions. See my permissions setup below.
groups:
Member:
inheritance:
- default
permissions:
- modifyworld.*
users:
'[buildCraft]':
group:
- Member
'[industrialCraft]':
group:
- Member