Is it an old field ?
Because since Cook 2.0, the JUser field is considerated as a regular FK. (before, it was a special field type)
So you may have a legacy JUser field instancied when yuo reopen old projects. It should work the same, using automatic default field names.
Try to recreate it in the builder with the same name.
If you delete/create with the same name, the dataset will restore intact.
EDIT : I putted in FAQ, not because it has been asked oftenly, but because it is important question. Thanks for asking.
I guess you experience this problem. If not, can you open new topic so we can leave this answered question here.