I was using about 10 quarries in my world, when some of the running ones started decaying. They still ran, but the frame slowly decayed .

Seen here are quarries that are running and decaying at the same time.
http://imgur.com/a/EOuYs#0

When you remove a quarry it will tag all frame blocks connected to that quarry. If two quarries have frames that touch each other and remove one, the frame of the other will start to decay. To avoid this, don't put quarries that close to eachother.

@Krapht I would still consider this a bug, that needs fixing, rather then explaining people how to not run into it.

I haven't removed any quarries, only their power. Also, when I logged back in the problem went away, seems to be odd behaviour that isn't reproducible.