It looks like an indent at the end of a code chunk interferes with the splitting of cells in the resulting notebook. MWE:
In "test.jl":
# Some text
a1 = [1 10 2 20; 3 30 0 0]
#- this works to split
a2 = [1 10 2 20;
3 30 0 0]
#- this doesn't
a2 = [1 10 2 20;
3 30 0 0]
a2
#- This does
println("What?")
julia> Literate.notebook("test.jl", "./")
[ Info: generating notebook from `~/computation/julia_playground/intro_julia/test.jl`
[ Info: not running on Travis, skipping links will not be correct.
[ Info: executing notebook `test.ipynb`
[ Info: writing result to `~/computation/julia_playground/intro_julia/test.ipynb`

It looks like an indent at the end of a code chunk interferes with the splitting of cells in the resulting notebook. MWE:
In "test.jl":