Water-based poly can have adhesion problems when applied over an oil-based stain that's not thoroughly cured. That's why you should always apply a barrier coat of dewaxed shellac to seal oil-based ...
The Family Handyman on MSN2mon
How to Apply Polyurethane
We use an oil-based polyurethane finish in this story, though you can also use water-based urethane finishes ... with a flat ...