I'm curious, are you enabling modifyworld, and if so, what permissions do you have set for the entities like buildcraft, ic2, etc etc?
See I use most if not all of the above plugins everyone has listed, except that I have modifyworld turned on for finer tuning of what my users can and can't do. Keeps the builders in line, if you know what I mean. But the issue with ModifyWorld is that it doesn't allow the quarries and mines to do their stuff because of the way they are treated as players.
I had trouble finding the config once before, but can't seem to find it again. Therefore I was wondering how you had your permissionsEx yml set up.
Thanks in advance,
Zhiv
EDIT:: I found the pastebin with the example permissions nodes. I'm sharing it in the hopes it may help someone else as well.
http://pastebin.com/uLF1FA4G