Im having the same problem, no one has answered my thread yet but i don't know why because the steam engines are used to activate the quarries and combustion but i used them both but they start to pump like they do but the frames are supposed to start joining into a massive cube frame but it isn't working. It maybe because im using different plugins that could affect it.
Plugins!
ChatManager
craftscripts
essentials
mcMMO
MineBackup
MobDisguise
ModifyWorld
PermissionsEX
PluginMetrics
TreeAssist
WorldEdit
If any of these plugins are to affect the quarry please let me know because the quarry is the best out of buildcraft and i really need it working for my project with my sister!
If this problem doesn't get sorted out i will downgrade for a bit until this is sorted