@DanteLives
Thanks for answering all the questions!
I've some new questions, but first something you might have tried already:
What happens if you check opaque water (where for others unchecking/not checking is a solution)
If that long shot didn't work:
Are all, your computer, Ubuntu and your minetest 32 bit or 64 based? (I have very little knowledge of this, but understand it is best when all are the same)
Since it is a package I assume it is installed system wide.
Are you willing to try to compile/build minetest yourself as a run in place version?
I use (copy) the instructions for Linux in the readme.txt
https://github.com/minetest/minetest .
(you probably need to type sudo before being able to install dependencies)
(you need to type/copy the minetest version number that appeared in your folder, stead of using the 286edd4 -example)
Before doing this, you might want to run this command in the terminal:
sudo apt-get install build-essential to be able to compile minetest.
Just to be complete:
Do you have these lines:
WATER_ALPHA = 160 (line number 6)
in
minetest/games/minetest_game/mods/default/init.lua
alpha = 0, (lines 20 and 53)
in
mods/sea/noairblocks/init.lua
P.s. I made a run in place build of the 0.4.10 stable (with 0.4.10 minetest_game stable) from the Github ressources and couldn't reproduce the airblocks you have).