I had a similar problem recently when I updated a copy of the NPL that I had checked out some years ago. It was checked out of an older location for the NPL which is no longer being updated. Make sure you have the version checked out from the correct CVS archive.
One way to check is to look at the CVS directory in the main directory of the NPL. Look at the CVS/Root file and see if it ends in cvs.webwork.rochester.edu:/webwork/cvs/npl and not something else. If it is not from the npl archive, check out a new copy and run NPL-update again.
I think this may be your problem as your directory is called database_problems which was the old name; the new one is NationalProblemLibrary (in the documentation; see http://webwork.maa.org/wiki/National_Problem_Library).
Hope that works for you.
Updating NPL - did it really happen?
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