Are your MT boxes bridges?
Hmmm. I don’t think this is a known problem with Mikrotik. What version are you using? The only thing I can thing of is either the machine you are using to connect is preventing proper connection due to a firewall setting, that you are port forwarding to these and you don’t have the secure port for winbox setup, or you’re blocking the secure port on the MT boxes themselves. I ran into this a few times way back - make sure you aren’t blocking port 3987 (or whatever 2.9 uses if using that version). Have you verified this problem happens on different computers?
Also, have you tried redownloading winbox from one of the routers and deleting your old winbox.exe and plugin files?