Jami, we have discovered a bug in some of the careers that seems to be caused when career upgrades are purchased. When a peep is affected in the manner that you describe, they should return to normal the next time you purchase a career upgrade. I'm not sure when we'll have a fix for this issue, though.
Mayfly, you are correct about the way working and pay operates. Here's how it breaks down:
Each time they finish a work cycle they will receive a small amount of money, which may not even show in the bank balance until they have worked several cycles if their salary is very low (e.g. 15 coins per day), since the amount must reach the next full coin increment to be displayed. The game tracks fractional coins, but doesn't display them.
In addition to this small payment for completing a work cycle, they receive a portion of their current daily income in regular payments every hour of the day.
I hope that helps everyone!