Your problem seems a little bit strange to me.  ???
Even if you use a filter, the machine should be decalcified regularly. The machine shouldn’t be decalcified as often as without using a filter. But all 1000-1500 cups it should be done.Â
Unfortunately Jura does not write that into the operating instructions. >:(
Therefore most users think that their machine with filter needn’t to be decalcifyed.  😮
-mistake-
The most frequent error of these machines are problems with calc. 😉
It also could be that your temperature sensor isn’t tightened well to the heatingsystem.
….but try decalcifiying first…. ;D