Yoshi's Story level backgrounds regression

[IronYoshi64]

I notice a very distracting line of misalignment/glitchyness in pretty much all of the level backgrounds in the game. Some more noticeable than others.

I have tested this in both 32bit Project64 and Mupen64plus for Windows, both have same problem. I tried several newer builds of GLideN64 to see if it is still there, and it is. The last build I notice that this is NOT an issue in is the GLideN64_5b515a5a build, back on Aug 28. #2037 (comment)
This issue does not exist on Public Release 4.0 either.

Here are some screenshots on different levels where I marked where you can see the issue with red ovals.

Practice stage:

Jelly Pipe:

Tower Climb:

Jungle Hut:

I will be more than happy to provide more information if anyone needs it.