I own the game Stellaris on Steam and on GOG. At first, I only owned the game on Steam. Everything in GOG Galaxy 2.0 seemed fine at that point, tracking game time, achievements, etc.

Then, I got the game on GOG along with a couple of DLC because even after re-buying Stellaris, it was cheaper than buying the DLC on Steam, and I don't particularly like Valve/Steam anyway.

Then, I had both the Steam and GOG versions of the game installed. After playing the GOG version, if I right-clicked the GOG Galaxy 2.0 icon on my task bar and chose to run Stellaris from the "Recent" games context menu, it would run the Steam version, even though I had launched the GOG version more recently.

So then I uninstalled the Steam version of Stellaris and removed Stellaris from the "Recent" context menu list.

Now, no matter how many times I run the game, it never re-appears in the "Recent" context menu list when I right-click GOG Galaxy in my task bar, and I don't think it's updating my time played, either. As I play more game titles, Stellaris just seems to move further and further down the list when I sort my library by "Last Played," even if Stellaris is the game I launched most recently.

It's as if since I had and used the Steam version first, my GOG Galaxy library is just ignoring anything I do with the GOG version of the game and only tracking the Steam version that isn't even installed anymore.