When I try to move the origin box position over the layer, while I hold the left mouse button down over the green dot, with the cntrl button pressed, the box moves the position of the layer instead of moving over the layer. I never had this prob in earlier versions of Synfig.
Thank you.
I confirm, it seems this has changed between 1.3.11 and 1.3.12 
(at least for origin of Group Layer)
morevnaproject commented on Oct 10, 2020
Hi! This is an expected behavior. User now should drag violet control point (right under green control point) to change origin. 