Yes ...the case fan will no doubt be thermally controlled if it's connected to the motherboard .... and obviously something has gone wrong with the sensor. Have a look round and see if there are any other 2/3 fan connectors on the motherboard you could use. Most times there's the "cpu fn" (we don't want to disturb that one!), "sys fn" and one or more "case fn" connectors, but being a bespoke motherboard in that SFF case you may be out of luck. You've already hooked it to 12v to get it working so it wouldn't be difficult for you to wire it permanently to a spare power connector (you will probably have to cut the cables and rejoin them). However bear in mind that the fan will then run continuously.