I did some testing, and I think the time it takes to earn another round of cash from your owned buildings is right around 15 minutes. Unused time doesn't seem to carry over between restarts of the game, so if you play for 5 minutes, shut it down, and load the game later, you'll still have to wait a full 15 minutes for more money.
There's only two things that stop it:
- Hitting the "Transfer Limit" which increases as you gain city income. This is a multiple of your money-per-unit-time value, and it's just there to keep you from leaving the game on overnight to make mad cash.
- Pausing/quitting the game. If the game isn't running, you don't gain money.
If you thought you got "paid" twice in quick succession, it's possible that you had money laying around from a previous bank transfer that you hadn't picked up yet. There's no "push" notification that money's available, so you might have taken money out twice 5 minutes apart, even though it was really 15 minutes of clock time between times you actually got paid.
"Game time" is a bit weird. I don't know if my sample running time was too small, or if the game rapidly transitions between times of day at certain points, but I took a save just after the climax of Act 1 and let it run for about 40 minutes, and the sun stayed in the same spot. A 15 minute test of my cleared save yielded similar results. However, I'm certain that eventually, time passes and there's a day/night cycle. It's possible that, as others have speculated, it doesn't pass until late in the game, but I feel like I've seen this happen earlier in the game as well.