No matter what type of dithering is selected, it always defaults back to “no dithering” as soon as I click anything, thus, making any type of dithering with the gradient tool impossible.
Changing back to the old version, v1.2.4 resolved the issue which makes me think it’s a new problem only in v1.3.
I’ll be using the old version for dithering-related things until then, but I really wish it’d get solved.
The workaround I tried in v1.3.1 was to select the pencil tool, go to dynamics in the context bar, and turn off Same in all Tools.
I was also able to set the gradient’s dither matrix from the dynamics dither matrix menu.
Also an option: change the aseprite.ini file while Aseprite is not open. It can be located by going to Edit > Properties and looking for the Locate Configuration File link under the General tab.
From the Steam forum:
Today we’ve released v1.3.2, this issue should be solved 
