This behavior seems to be happening when you are decrypting several Cryptomator vaults in a different order each time or have other disks/flash cards changin the order of the disk letters., because Cryptomator automatically assigns the next available drive letter to the newly decrypted vault.
You can right-click on the locked vault in Crytomator → Show vault options → Mounting tab → Select Use assigned drive letter → Choose some never used drive letter in the middle of the alphabet. Then open Obsidian, activate plugins once, and every time you re-open this vault they will be active. This works when you are synchronizing the folder between the computers as well, you need to set up Cryptomator similar way everywhere.
Hope this helps. The same thing bothered me quite a lot.