Gary, the finish coat should not re-wet the sanding sealer, even if both are water based. I suppose it could happen if the sanding sealer was not allowed to dry enough before applying the paint, or there was something wrong with sealer. I've done tons of finish work over the years (including car and boat painting) and have never seen what you describe on a properly prepared surface and using the right materials. It could be your sanding sealer is too old, but I doubt that is the problem.This is what I have been using. And I think I've figured out the issue.
This sanding sealer is water based & so is the paint ( krylon acrylic ) so I think the paint is "re-wetting" the sealer
I'm not a fan of Minwax products. Varthane makes a decent product and is readily available. As others have noted, it's hard to beat dewaxed shellac. It's gotten harder to get fresh shellac these days, since Zinsser Bullseye stopped putting the mfg. date on the can. You can get shellac flakes at most woodworking stores (e.g., Woodcraft & Rockler) and dissolve/mix your own. Just be sure the flakes are dewaxed. I use shellac sealer under Sherwin Williams CAB clear lacquer and sometimes use it under their catalyzed lacquers (think white kitchen cabinets) (available at industrial sales only). Vinyl sealers are great, but they are pricey and can be hard to find. Sherwin Williams has one, but is spray application only It's a vinyl modified nitrocellulose product that doesn't have to be catalyzed, but should be for best performance.
For those who might not know, Zinsser Bullseye sealer is dewaxed. I don't use their regular shellac finish, but if memory serves, it is not dewaxed. Non-dewaxed shellac is designed as a finish, not as a sealer - even if you thin it with alcohol.