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Actually, there is a way you can explain it such that it makes sense that it makes no sense.
Hyperion could be an inefficient cluster**** of a corporation--it could just be that bureaucracy and miles of red tape make it difficult to revoke New-U privileges.
After Roland started the resistance against Jack, Jack probably found out they had New-U access, and started filing the appropriate forms; a few years later, shortly before the beginning of Borderlands 2, they finally are cleared and the original Vault Hunters lose the ability to respawn. He submitted your forms after you defeated Wilhelm, as well, but they never got through because he forgot to fill out box 4 on the second page and failed to submit them notarized and in triplicate.
The Bureaucracy yields for no man, not even Handsome Jack.
This is my headcanon going forward :smallbiggrin: