The question is whether he comes on time.

Literal

Problem [copula-な] [nom-の] [topic-は] he [subj-が] on-time [to-に] comes [whether-かどうか] [copula-だ].

問題なのは uses explanatory の — 'the thing that's the problem is...' 時間通りに ('on time, as scheduled') uses ~通り ('in accordance with') with adverbial に.