Just like gut, the New Nylgut® is liable to suffer from cutting edges. Before stringing the instrument do make sure the nut and bridge are free from sharp edges and the nut grooves not too deep and perfectly smooth. You can get rid of sharp edges with very fine grit sandpaper (600, for example) or the finest steelwool (000).
The best sound quality develops when the strings have completely set, which may ordinarily take sometime. To achieve a stable intonation in just a few minutes you can repeatedly pinch each string at midlength with your fingers, pull it decidedly sideways and tune it up again. Stop when the string does not pull out of tune anymore.