This setting is the issue: "Use the players xp (not the level xp) to calculate loss": true,
Example:
The player has 300,000 xp.
The xp threshold for the players current level was 275,000 xp.
The next level up is at 325,000 xp.
The UI shows that the player requires 25,000 xp.
This means that the player is 50% through their current level.
Scenario:
If the above config setting is set to true and the player dies, the plugin will calculate the xp loss based on the players TOTAL xp (in this case 300,000xp). If it was set to 20%, then they would be losing 60,000 xp. Since Skill Tree does not allow you to lose levels, It will either: put their xp back to the start of the level (275,000 xp), or put them back to the start of the level, and add the rest as xp debt (35,000 xp debt).
If the above config setting is set to false and the player dies, it will calculate the loss based on the current level threshold. In this case it would be 50,000 xp (325,000 - 275,000). This means that the player would lose 10,000 xp, putting them back to 290.000 xp.