I thought that the issue was only with Winbox/netinstall.
If you don't have connection at all (without the interposed switch) it could be what you are suspecting (something in the cabling, but everything - including the Mikrotik and any laptop built in the last (say) 15 years is automatic MDI/MDI-X).
The fact that your other (old) laptop works fine should confirm that the auto-sensing is fine, at least on Mikrotik side.
Your configuration is pretty much standard AFAICS the only "strange" (to me, likely normal) is the "/disk settings".
You can try (not that it will necessarily give any useful results) the Mikrotik "cable testing" feature, see here:
A possibility is that one of the RJ45 plugs on the cable you are using fits "loosely" on the socket (either of the laptop or on the RB5009) while it fits ok in the switch, but then your other laptop should have the same behaviour, and if the issue is the socket of your laptop, it shouldn't work when you use the switch in between.
It could be an issue with auto-negotiation between 100 Mb and 1 Gb?