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Not sure why this is happening, but when my players teleport between dimensions, they lose all their XP. In some rare cases, they can actually exploit this and duplicate XP. Not sure where this issue is deriving from.
Since you have bukkit, I would like to see a list of plugins.
You probably have Multiverse setup;
this has a setting that would move players from one world to another with two separate inventories.
This would mean you would get the experience back when moving back to the other world.
Is this the case?