The phrasing in the DMG seems (to me) to indicate Seeking weapons would work against any miss chance, including Entropic Shield or Blink. Is there disagreement regarding this?
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As Written There's No Disagreement...
The seeking weapon special ability has the effect of "negating any miss chances, ...such as from concealment" (DMG 225). Honestly, that's about as absolute as this game gets.
...Unless the DM's Really, Really Out to Nerf It
The only disagreement I can see arising is that the spell used in the manufacture of the seeking weapon special ability is true seeing [div] (PH 296), which explicitly "does not help the viewer... spot creatures who are simply hiding." A DM who's very, very angry at a an archer ignoring miss chances on his creatures could on that basis house rule that the seeking weapon special ability can't overcome mundane concealment because the spell used in its creation can't either. That's a really mean house rule, though. Archery's hard enough as it is.
"What If the DM Does Do That?"
The spell corpse candle [conj] (SpC 53) reveals hidden creatures.
If it is writen as a miss chance, a seeking weapon will ignore it, but it is better to study individual effects: