Bare bottom tanks hold bacteria closer to fry so a small layer of substract helps here.
If the males breed repeatly he lose's condition so he's waste that the fry eat won't have enough good stuff for fry to eat.
If the tank has had a few spawns thought it before the tank mighten have enought small algaes to feed of causing the fry to starve.( more surfaces algae can grow the better )
Some ideas to improve fry chances is to feed more often in smaller amounts,
add small layer of substrate (first clean bottom glass with a scruber and suck out all film build up,give male a 2 month break and feed up.
Filters and powerheads as long as they are working don't make alot of difference with BN's as long as it can handle the bioload of the tank load of fry.( i've had up to 600 in a 3 ft and not alot of current )
Main thing in in fish keeping is the water conditions,change often if fry present,10- 20 % daily for heavy load,ph to be stable,keep records to see if your doing something wrong.
Extra things that can help is to have driftwood in a bucket in the sun than keep swaping with the tank one's if limited room.( i use 20 small to medium pieces in most tanks )
Buy organic vegatables or grow your own and use a veried diet.
I tend to leave all fry in main breeding tanks with parents, ( commons ) in tank with parents i just remove male from tank when male needs resting,
i have had all most 1000 fry in some tanks and still doesn't effect breeding results.
I have mollies in tanks to help in breeding if this is in help for others.( the mollies have been in tanks for years and have lived happy down to ph's as low as 5.6 )