Where do the T-1000 machines come from in Terminator Genisys

This is not easy to answer outside of the context of the storyline as a whole. To answer this we have to start at the very beginning.

The original Terminator movie offered a consistent causal loop or, more specifically, a Self-fulfilling prophecy in which John Conner sends his friend Kyle Reese back in time to protect his mother, where in turn Reese impregnates Connor's mother allowing Connor to be born. Who, in turn, sends Reese back in time... I'm sure you get it, but it had to be pointed out. The existence of this causal loop indicates a certain predestination which is strongly tied with religion.

In the sequel 'Judgement Day' that followed we see they continue along this same path of [causal loops][2] and predestination. The remains of the original terminator (Schwarzenegger) from part 1 are being used to invent Skynet itself. The 'birth' of Skynet is elevated to the same level of John Connor's birth. The births of these two can be explained by many religious beliefs in which there is going to be a predestined fight between good and evil which will usher in the apocalypse, e.g. prophecies of the [Last Judgement][3] preceded by the [Second Coming][4] or the old Norse prophecy of [Ragnarök][5].

In 'Judgement Day' Sarah Connor is struggling with this apparent truth of predestination. On one hand she tries to prepare her son for the coming apocalypse but on the other she denies the concept of predestination and holds on to the idea of 'no fate', which she carves into a table. The fact that she prepares John Connor for the coming apocalypse and John's interaction and thus knowledge of the machines will make him the leader of the resistance, creating again a causal loop.

This makes for an interesting development because now, whilst staying true to the original timeline in which John Conner effectively creates himself and his own future, the timeline gets changed, which contradicts the idea of predestination. This contradiction relates back to the religious theme of 'Judgement Day' in which an apocalypse is inevitable but the outcome is not yet set.

In pt. 3 'Rise of the Machines' we stay in the theme of apparent predestination whilst changing the timeline again, both acknowledging and contradicting the paradox of this same predestination.

Pt. 4 'Salvation' we see the paradox unfold from a future perspective. We see the 2018 version of John Connor creating the original timeline which led to his existence in the first place. The title of the film 'Salvation' again refers to a religious context. I'm close to answering the question now but it's still worth pointing out that this movie in itself, with the sacrifice of Marcus, shows a strong connection with various [messianic][6] stories.

Finally in Pt. 5 'Genisys' we come full circle where the timelime has changed so much that the original storyline of the causal loop is no longer viable. The birth of Skynet has not happened when it was supposed to happen finally introducing the concept of the [alternate timeline][7] or [multiverse][8], a common theme in sci-fi where changes in the past branch off into alternate timelines.

It now becomes clear that there has been a multiverse all along, with every change made in the past created an alternate timeline with the same inevitable outcome. In part 2 the T1000 is sent back in time to kill John Conner, this is a result from the events in the original movie. 'Genisys' introduces the idea that, by meddling with the timeline, the story of the original movie is changed in such a way that all 4 prequels no longer stand. It is therefore the T1000 is able to arrive in a timeline where 'Judgement Day' no longer happens.

It is at this inevitable point in time and space where the whole idea of predestination gets obliterated. John Connor becomes Skynet because every alternate timeline has led up to this point; a point in which there exists both order and chaos; the final outcome in the battle between good and evil. When Skynet gets destroyed we start a new timelime in which the apocalypse has been averted. This new timeline can be tied to the title of the movie which is obviously derived from 1st book of the bible 'Genesis'(Latin) which translates loosely into the 'beginning'. With the destruction of Skynet there is a new beginning and it seems there are again endless possibilities and no predestination. The last few seconds of the movie give a glimpse of Skynet being still alive which again suggest there is a certain predestination towards an apocalypse and a final day of judgement. This last concept of a (never ending) cycle of beginning and end can also be found in Buddhism and Hinduism.

Ultimately all movies combined wrestle with the concept of beginning and end, life and death, and the ultimate question of life; whether we are plunged into a chaotic universe or if we are predestined pawns in the existing everlasting order of all things.

Because of my reputation I can't post more than 2 links, so you can look some of the stuff like causal loop up yourself :-)