ok... so here goes,i shall try and explain in the basic terms..
A fish tank is an ecosystem... there are microscopic bacteria that will live pretty much everywhere in the tank, (except in water) they basically consume wastes... if wastes are allowed to build up (even in an external filter) and there is not enough bacteria the water may become toxic to fish and other aquatic organisms.
basically with no fish in the tank there was little or no waste. so the bacteria were growing slowly if at all... it takes about two weeks for a tank to get a good amount of bacteria but i believe this is when waste is present... if you had plants and wood etc it may speed up..
So in your case.. two weeks was good but not much bacteria is present.. in time it will be, the guppy is a hardy (resilient) fish so it will likely survive.. the fry may not i'm afraid.. all you can do is wait for the bacteria to build up. Keep doing regular water changes of water that is around the same temperature as the tank..
And make sure it is treated with aqua safe.
The water will likely clear up in a week or two at the most. Keep doing ph/nitrite and ammonia checks every day or two and let us know if the levels are high (or low for ph)
Then when they seem normal for a while you can leave them and do them once every two weeks or so.
(it's not good i know but i haven't done one in my tank yet and it's only been running 4 weeks
Naughty me)
I guess it's just because i know the cycle has happened... the water is crystal clear. and the fish can handle a nitrite spike, on top of that i've been doing regular water changes and keeping a close eye on the fish's behaviour.