seems that latest updates really messed up the order of the resourcepacks.
using 21.0.6 for fabric mc 1.21.1

Since 21.0.3 the ordering is actually fixed!
It does now respect the order from the config, and is no longer randomized/alphabetical.
You may have to adjust your config to make use of that, rather than renaming the pack files.

I was always using this mod to load datapacks not resourcepacks as i prefer to manually organize them since i got my own way of doing that for my own sanity. But since that version, this mod is messing up the resourcepacks screen by not having available packs in order. I mean if i disable the mod, everything will be in order as it always were. If this is intended or wont be fixed please let me know.

Oh, you mean resourcepacks added trough vanilla?
The mod does not touch them. That list is provided by vanilla.
I can check whether I am accidentally mixing the list, but I hope not.
Until it's fixed you can also just use an older version.

I just tested it, the mod does not change the order of resource packs that are not added through the mod.
Could you maybe share your mod pack with me so I can debug in that?

Cant share atm but 2 days ago I did try with a fresh instance with the same resourcepacks, i think i couldnt reproduce it.
I also tried with the same instance removing mods to a point that all mods were disabled but still the order was messed up. (But I have to remind you that disabling the mod, all RPs were again in order.)
I also noticed in a fresh instance with just global packs and fapi, high contrast and programmer art RPs are on top instead of bottom. Maybe that could help?