Yesterday Clem removed
the ability to upgrade packages from Synaptic:
Removed the ability to upgrade packages (Synaptic isn't aware of safety levels and that's required for UI, but more importantly the selection of packages is buggy, the first CTRL+A for instance calls the resolver as if each package was to be upgraded individually as opposed to calling the upgrade on the selection as a whole. In the case of some updates, such as the recent mesa updates, this leads to the removal of clutter, and therefore totem and even Cinnamon.).
What I've highlighted is the possible cause of the issue you've stumbled upon.
On the other hand, mintUpdate correctly processes the whole selection of packages to update. After that, it calls Synaptic to perform the update. It is safe: Synaptic is only used as a tool to fetch the packages and apply the updates, not for performing the selection.