I don't really know how to answer you right now, since another user mentioned that both my and Duolingos translation of Το παιδί πρέπει να τρέχει is wrong, and that our translations would require the original Greek sentence to be Το παιδί πρέπει να τρέξει (i.e. not να τρέχει but να τρέξει). He also mentioned that πρέπει can be translated to should (but not in all cases, since if your mother says πρέπει να πας σχολείο she probably isn't telling you that you should go to school, but rather that you must). Anyway, since I am in way over my head here both with the Greek and the English maybe someone else can give you a proper answer...
I'm not sure how you can tell that both verbs look like subjunctives -- the present subjunctive is spelled just like the present indicative nowadays.
But yes, they're both subjunctives.
να τρέχει is the present subjunctive and it's used for things which are repeated, habitual, or continuous.
να τρέξει is the aorist subjunctive and it's used for things which are viewed as not having internal structure (beginning, middle, end) but are viewed as a single whole -- especially one-time occurrences.
The aorist tense often has a -σ- in it (and is then called a "sigmatic aorist"); this sigma can combine with other sounds, and with chi, -χσ- (which would have been -kʰs- in Ancient Greek) turns into -ξ- (-ks- in both Ancient and Modern).
Πρέπει να τρέχει means he has to run regularly, πρέπει να τρέξει that he has to run once (probably now). Both are possible.
It is not only subjunctive every case in Greek (past future ...) has two ASPECTS: One for a prolonged/ continuos παρατατικός action and one for an indefinite/ aorist/ αόριστος.
Present has only prolonged aspect, therefore it gives the prolonged stem: τρέχ-ω -> τρεχ-.
The indefinite or aorist stem can be taken from past simple = αόριστος: έ-τρεξ-α ->τρεξ-
For subjunctive this gives πρέπει να τρέχω/ I must run (and run) or πρέπει να τρέξω/ I must run (a little)