I’ve also been experiencing this problem or something very very similar.
When taking the initial 3 images the image on screen doesn’t always appear to update, this also happens during the ‘adjustment’ phase. It did, at the adjustment stage, seem to be connected with whether I clicked on the darks option or not. Ekos seems to carry on working sp it doesn’t seem to be a crash or at least not one it doesn’t silently recover from and not using the darks option does seem to allow things to work.
Must say the latest version does seem to have some oddities in this area.