So I changed the prime tower type, I guess it defaults to the new one that was added in the last firmware, I do not think it works right. but after changing the type back to square I think, I have no issues.
I managed to get the issue go away (and back) by changing the priming volume and/or tower width. The bug appears to occur only with 30 mm width and 45 mm3 prime volume (at least on my model). Any other combination slices without the issue.