My mage character is a master level conjurere and Im stuck with "Reanimate Thrall" active effect even though I dont have it anymore. I can summon two other things but the reanimate thrall is still there. Also it apparently causes any summon spell to fail about 30% of the time. Is there any way to remove the active effect..console command or something?

You could try opening the console, clicking on the summon and writing 'kill' in the console.
Or getting the banish summon perk for conjured weapons and hit it (may undo the perk changes later using removeperk and addperk to get another perk instead).