Yes they would be reproductively isolated.
Why do I think so? Well, bats and birds can't interbreed, and neither can dolphins and sharks, and each pair have evolved in worlds with exactly the same early-earth conditions, to fulfill roles which are exceedingly similar to their other half (two animals evolved for flying, two evolved for swimming, of similar size and shape and similar sorts of "successes" I guess would be my term, and yet totally different). Even better, they share the same historical conditions with exacting precision, and a fair chunk of familial resemblance from their very-base level processes from their shared ancestors, which is above and beyond what your question requires :)
And so, if bipedal hairless monkeys evolve again from this simulation, to fit the niche of thinking predators who adapt the environment to them rather than the reverse and then tinker with the world... they would probably have less in common with human-people than a bird and a bat have in common. Evolving flight (and evolving into all the niches) is probably not more of an overlapping niche, or indeed more of a specialization, than what human-people have done.
Evolution on earth was driven by a lot, a lot of factors - including geography, local conditions, and each other. Some of which are factors we don't know. some of which are factors we can't recreate or influence, and some of which are factors tightly correlated with adapting to changing circumstances (again, including each other). we can't even run a stimulation of earth's historical conditions without running into patches where we're not exactly sure what was going on or which factors led to which results, and you would as a preliminary starter need to be able to perfectly reproduce them.
If you sent an exact replica of (early) earth, accurately programmed to change for every variable earth underwent - including cosmic radiation, precise light and gravity fluctuations, minutiae of geography including volcanic eruptions and tetonic movement, extinction events (and who/what survived and didn't), meteors and such, the moon - you still could not guarantee humans, because you can't monitor interactions of the evolving creatures with each other enough to insure evolution stayed "on course", and if you could any intervention would be "taken advantage of" or, hm, adapted around, to change the actual results.
The godling of the simulation favors primates, so now you have a thousand and a half extra primate species that survived thanks to its intervention - oops. Or else it knows dinosaurs are supposed to evolve and then go extinct, except it was juust a leeetle bit too good, and the predecessors to alligators, or some other lizards, or birds, now didn't survive, either - oops. Ah, wait, it knows that horses are gonna be really important, better make sure they don't get lost - and horses can now afford to be a little slower, a touch more arrogant, taking advantage of this invisible protection instead of getting better, and we end up with non-domesticable unicorns or thirteen extra species of zebra, instead of the horses we could breed for work and travel.
And in all those altered initial conditions and interactive shenanigans, the precursors to humans never get off the ground, or become something slightly different, and whatever ends up taking the human-people's niche (if, indeed, anything ever does) need not be any more closely related to us than a dolphin is to a shark just because they both swim and eat fish and can't stay still underwater too long or without drowning.