I have not had any issues using all four slots on the Z400s with GPUs.
A large portion of my systems are 4x Geforce 1060 -- with one card in the bottom x16 slot and risers on the other three. As pictured:
----------
The splitters also do seem to work fine as I have a few systems with 6x 1060 or 1x 1060 / 5x 1050Ti using splitters.
What splitters are you using on that system? and link to buy
Mine are 4x GTX 1070, all 4 risers, no problems
I have used two types -- this type I've had in operation the longest:
https://www.amazon.com/gp/product/B073W9KCFC/ref=oh_aui_search_detailpage?ie=UTF8&psc=1
I use the bottom PCI-E slot for a video card -- just like the 4 card systems -- and the top two slots for one splitter each (two cards per splitter) -- and the third slot down has the riser plugged right into it.
I can get a few pics if you need.