I had very similar problems, on my first checkout dive i didnt equalise early or often enough (in laymans terms, at the surface, before descending and about every 1-3 foot til at least 15ft and probably every 2-5ft from there down) and got a little pain, ascended and equalised again before going down. I didnt have too much trouble after that, but on surfacing between the 3 dives and on the way home my ears were similarly still stuffed up. Saw the ENT before doing the 4th checkout and he suggested i had some fluid in there, essentially replacing the pressure that was outside the ear (during the dive) from what i could gather.
Since then i have completed a few more dives, each time the surfacing was a little muffled, but no pain on descent, ascent or on the surface, just dulled hearing for up to a week. Tried to clear this with sudafed to clear congestion if there was any, ibuprofen to counter the inflamation if there was any in my eustation tubes and lying on one side at night to get my ears to drain thru the eustation tubes. The length of these post diving boughts has reduced over the number of dives, but is still there. I meet people all the time who have similiar problems, also slightly bloody snot as well - no infections of anything, just phlem like stuff. I try not to dive whilst i still feel this way, and the bouts seem to come in during the drive home rather than immeadiately at the surface or on the boat, which is very delayed!! I had a warm rush of feeling in my ear this last weekend, which i assume is blood or other fluid, i didnt get vertigo, pain or get sick, so i am pretty sure there are no inner ear troubles, and on swallowing i can hear a small amount of clearing (popping and crackling) each time. So at the mo i am battling that one and just asking people to speak louder while i wait for normal service to resume. Never actually 100% sure it actually goes away - maybe i have become more aware of it and therefore still anxious about it.
I would suggest seeing an ENT if you can, particularly if things dont improve in a few days (like i said, mine takes from a few days to a week to clear - getting less now after a few dives), just to make sure things are ok, mine had a chat with me, but could not really help, he suggested that it would improve, taking sudafed and generally stearing clear of pressure til it went away.
Another thing that many suggest is that you should equalise using the pinch and blow method, that one doesnt work for me, i pinch and swallow or just swallow to clear - its also easier.
I will also steal pipedope's wind as i take his message and include this:
"I also tell EVERY DIVER to go watch the streaming video at;
http://faculty.washington.edu/ekay/index.html
"
Streaming Video Lecture
"The Diver's Ear - Under Pressure"
Can be helpful, there are other things on different methods if video isnt available on your connection (or is really slow) at Rodales:
http://www.scubadiving.com/article/0,7424,3-40-122-70,00.html
and DAN:
http://www.diversalertnetwork.org/medical/faq/faq.asp?faqid=123
Hope those help, but if you already know all these methods, then the sit it out and wait option is pretty much it, i wouldnt dive when feeling all bunged up in the ears (has been a close call to cancelling due to this before) and if you want to the ENT cant hurt.
Simon