Yes. . . and no.
If at least 5 days have passed, mining (and everything else that occurs on a construction tick) gets updated. It doesn't mean it gets updated every 5 days though.
As an example, lets say you have a colony you want to collect minerals from. That colony produces 12k minerals per year. That's roughly 33 per day. You automate a freighter to go to the colony and collect the minerals than return somewhere else and dump them. The freighter makes the full round trip in 11 days. Colony starts with 1K minerals.
You queue up all the orders, and run a 30 day tick. Five and a half days in, the freighter shows up and takes the 1K minerals on the planet. It only takes 1K and nothing else because the construction tick doesn't happen until the end of the interval you ran, even though more than 5 days have passed.
11 days (16. 5 from when you started) later it comes back to the colony. There is nothing to collect, the tick hasn't happened yet. Freighter cries in the corner that there is nothing here. Another 11 (27. 5 total) days later, still nothing on the colony, no construction tick, another failed collection.
Finally, another 2. 5 days later, the selected interval ends. Your freighter is halfway between source and destination, with jack diddly onboard. The colony processes it's 30 days of mining and vomits out just a fuzz under 1K minerals onto the colony.
It's entirely possible this is what's going on if you're running an extremely short route. If this is the case you have a few options.
1. Develop a much smaller freighter for this route that won't empty the colony in a trip.
2. Develop a much much slower, more fuel efficient freighter for this route.
3. Add a delay in the cycling orders of your current freighter.
4. Use the load minerals until full order.
5. Run 5 day intervals exclusively.
Personally I'm an absolute freak for efficiency, so I don't think I've ever processed a 30 day interval in over 100 years due to the fact that if a construction job finishes during the interval, the next job in the queue won't start until the construction tick processes and the job actually finishes. So if your job finishes in 10 days and you run a 30 day tick, your factories just took a 20 day smoke break.
