I basically have the same issue as the OP. Bison isn't working properly anymore ever since 3.3 and I'm sort of fed up with it right now. I've tried PhanxBuffs, but as good an addon it is, I actually want to see the remaining time on my buffs even if they're longer than 30 seconds and I want to be able to scale down the duration time, as the default is rather big for my taste.
Unless I'm overlooking some options in Phanx's, which I would love to be pointed out if I did.
@Vimes: For me the icons/text start blinking when the buff has 30 seconds remaining, which on itself isn't all that bad, but it's in a fasion where you just lose overview, and specially in pvp this is really, really annoying.