The issue of the ports not functioning on my CRS309-1G-8S+ switch only resolves after a reboot. I've tried a factory reset and setting the links to 1G or 10G, but to no avail. Is there a known solution to this problem? Why does the switch only work after a reboot?

I have no answer to your question.

I used RouterOS 6.* for quite a while and now RouterOS 7.7 on CRS309-1G-8S+IN with reliable results.
The ports stop working only if I command system shutdown or disconnect the power.
Consider booting RouterOS instead of SwOS which may add useful information.