Every time I restart my server, this happens:

http://i.imgur.com/zwLG8PO.png

The refineries cease to work. Potentially, they may even erase the content of their input tanks in the process. I haven't witnessed it happen directly, but they always seem empty after a restart.

Have to shift-click them all to make them work again.

Edit: This has been happening since roughly the "wooden pipe rotation changes when neighbor is in different chunk" fix, but is still current in 4.0.2.

Fixed in 4609d74