It looks as though you are using the current full release of the software (v2.9). There are some problems with the automatic calibration which are addressed in the current v2.10.0b1 beta release. In the server v2.9 the autocalibration can get confused. Usually it does complete, but the colour can be very wrong, especially if the lighting becomes much brighter or much dimmer than the last calibration. If you update to the current beta, the disable flat-field correction button works to remove the autocalibration, there is also a separate auto gain and exposure button to set your sample exposure without needing to play with the camera settings manually, and the autocalibration itself is very robust.
If there are reasons that you cannot use the new beta, then if you can find the json file which stores the autocalibration, removing that can reset the problem (I can’t guarantee it won’t just break the installation). Or I have resorted to re-installing the SD card image to start from scratch. Then make sure there is plenty of light before you first run the autocalibration.