ExUtils2 version: 1.12-1.5
Forge version: 2407

"I'm having an issue where the upgrades from exu2, as soon as the "penalty" text is updated, won't stack."

They are actually two different Item nbt tags/id's , so it's doing what it's supposed to do. The mod updated to have two different tiers.

not a bug exu2 speed upgrade only stack to 4.

yeah speed upgrades slightly different, multiple tiers, don't stack the same, etc