Same problem here. Initially set up with 3 Thermal Expansion steam engines, and they worked fine until i logged off for a couple hours.
Now both the steam engines and 3 stirling engines just sit there and store energy.
i have replaced all the pipe and moved the engines about and replaced the quarry.
Also have quit and restarted multiple times.
side notes: the stirling engines do not react to any of the wrenches?!?!
if i remove the engines and put them back in immediately they will not line up with the Wooden Con' pipes.
But if i remove the WC pipe and place it again followed by the stirling engine it lines up. found that odd.
Playing single player
Win 7, 64 bit
16 gigs of ram
edit: also, when i start up my world and pull the switches off of the above stirling engines.
i cant shift+click the levers back onto the engines!?!
To re-enact what i did: axe the engines, replace the engines, leave the chunk for the adjacent chunk, remember that that i need to replace the levers, go back to the chunk,
try and shift+click the levers on the engines. doesn't work?!?