I have exactly the same problem, it seems that I reached the max number of sprite collections i can create.
When I want to add a new one (I already have 9 collections), unity crashes, fatal error saying i allocated too much memory.
Even when i launch unity, the editor takes approximately 2 go of memory, and i can't do much inside the editor. I'm quite stuck with my project.
And also, i have pretty long animations (120 pictures), and i wan unable to add all the images inside a single sprite collection, i was forced to divide the sprite into 4 collections. Above 60 frames, the editor crashes. Computer i use is good (4 go ram, quad core, etc...).
I use multiple atlas generation (because final app needs to be high definition), compressed and size = 2048.
Help.
Thx.
Ps : great product anyway.