In answer to your question, normally fingerboards are actually not painted. They are made of ebony, which is a solid black material. I have seen a few fingerboards that were made of a different material and then paint was added, but this usually shows that the instrument is poorly made.
Fortunately the fingerboard has nothing to do with how expensive the violin is worth. You can get a new fingerboard put on, which is a little expensive, but worth the money if you have a valuable violin.
On the other hand I wouldn't worry to much, unless you are looking to sell the instrument.
Michael Sanchez
P.S. Can't wait to announce the launch of Violin Tutor Pro Series 2-5!