It's not a plugin fault. This is a default behavior of vanilla Morrowind (not happens in OpenMW, though).

"One or more plugins could not find the correct versions of the master files they depend on" ERROR.

This is caused by using different versions of esp master files or different dates. You can safely ignore it, but you need to press "YES" every time.

*Steam version of the game was used, by the way. But esp and bsa dates are equal to CD version, so that's can cause this warning.

Wrye Mash can fix that, so you not need to press YES every time.

You can find  Wrye Mash Stand Alone (Melchors WMSA version 003) here.
There is newer version around but this is a most stable one, I believe. Python is not required.

So, you need to install it to Morrowind directory. Then, run Morrowind\mash\mash.exe and select the plugin.
Then, Right mouse click on Morrowind, Tribunal, Bloodmoon on the bottom from the right side.

Answer YES to "Edit/update the masters list?" message and click "Save" at the very bottom (right after Morrowind, Tribunal, Bloodmoon icons)

That's it. Hope, that can help