Problem: shift clicking multiple items on the same type don't combine them into one stack, instead 2 or more stacks are created, when you click one of them, it combines them as if it was a visual glitch

How to recreate: new sp world, get some wood, split it into your inv, then shift click DRAG over the splited items so they go into your hotbar

Issue on Mouse Tweaks tracker

MouseTweaks-2.12-mc1.14.4.jar
secretrooms-6.0.1.jar
forge 28.1.39

I really don't think this is a secretrooms issue. Remove secret rooms and see if it persists.

If you check the issues page over at Mouse Tweaks, I did tested with only Mouse Tweaks, and there's no issue.

Update to the latest forge and see if it still happens. There is literally no reason that secret rooms would cause this, I don't mess with anything inventory related.

Also could you send a video / gif of the issue in action

Look, I'm just trying to help here :) , it's literally two mods, not very hard to check it out for yourself.
I've updated to latest forge, still happens.

Unable to reproduce. Try resetting your mouse tweaks config if you haven't already.