Can you hear characteristic clicking when the hotend gets clogged? You should hear that when the extruder is really clogged (it’s the sound made by gear pushing the filament when sliding). I had such a problem. After changing (or regenerating hotend) the problem was gone.
If you do not hear sliding gear than I would suppose that the hotend is not getting clogged but the material switch is not positioned correctly and the printer detects material jam. I experienced this problem. It appears only when printing in dual material mode. The printer changes the material by pushing material switch (in the head) on the bumpers on the left and right side of printer (I don’t know how they name officially these elements in Zortrax…). I noticed that the printer do not push this switch to the end. The material switch is not fully pressed. Sometimes the printer starts to extrude properly but the material switch may pop out in any moment, than the material could not be extruded and the printer shows error (material jam). Sometimes the printer could not extrude at all (the material switch is in the middle), printer show material jam.
You can easily check that: When the printer stops with the error message you can check if the material switch in the extruder is fully pressed right or left or not. If it is more or less in the middle than you have the problem with switching.
This problem is connected with X-axis layer shifting. Wrong positioning of the printer head makes both problems with layer shifting and correct material switching.
You can try “hotend switch calibration” procedure (Settings > Working options > Hotend switch calibration). In my case this procedure does not help.
I hope I copped with this problem by axes maintenance procedures. This one: Axes Maintenance in Zortrax M300 Dual 3D Printers | Zortrax Support Center I had some misalignment of printing guides (detected with use of jigs - guides were not paralel). I corrected it by this procedure: Axes Maintenance - Method with JIGS - in M300 3D Printer | Zortrax Support Center. I also tightened the screws on the gears on which the belts work. Now the problem is probably gone (I have still some other problem but the material is switched and extruded correctly).