i was hoping someone with more expertise would reply but looks like you're stuck with me!
When bailey had a sore ear I used Thornits once a week and it cleared it up great.
However, it came back a few months lather and I had to get cleanaural. This cleared his ear up nicely and i now put a dab of thornits in usually every month (or actually when I remember!) I've never heard of putting it in twice a day - hopefully someone can tell us if it's right or wrong but I personally wouldn't do it as it just seems to be too much going into his ear.
I think in this case I would go back to my vet & explain it has not cleared up and try and find a definitive solution. If, hopefully, you manage to resolve the problem i would pop a dab in once a month as you know what they say, prevention is better than cure!!