I haven't found a solution that works perfectly yet but I circumvented the 
problem by making a check for colons:

rows = inds[1] == Colon() ? (1:sys.ny) : inds[1]
cols = inds[2] == Colon() ? (1:sys.nu) : inds[2]

Not perfect since it limits you to always have to use exactly 2 incidences, 
but it works in my case. 

Maybe the handling of Array{Vector} should be looked at, seems to me that 
there are quiet a few cases where you run into problems with that datatype. 
For example, I don't think there is a built in way to transpose an 
Array{Vector, N>1}.

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