Well, I'm playing MotB right now, and this crap has happened in Ashenwood. When I cast it (9th lvl slot) it works as a usual 3rd level Haste. It actuallu pretty sucks because this spell helps a lot. Is there any way to fix it?

Some area transitions remove all magical buffs on your characters, regardless of their remaining duration. This makes the persistent spell feat very unreliable in practice. The feat is basically non-functional in Storm of Zehir, since that campaign has a lot of area transitions with relatively few encounters in each, so long-term buffs are largely useless.

Sucks, I know; persistent haste is awesome and this metamagic is pretty much the only way to make it last throughout the day (especially with the longer rest cycles that MotB encourages).