Looking at this post
from Dicky, who put together the convertor, it's unfortunately not possible to convert the passwords from punBB into phpBB. Since FluxBB is basically a fork of punBB, I'm going to assume that the same is true for FluxBB. Your users would have to request a new password in phpBB. You could add a global announcement or send a mass e-mail on your board to make your users aware of this.
Dicky wrote:As for the passwords, phpBB and PunBB use a different encryption schemes. There is no way, as far as I know, to transfer them so that they are usable.