Problems with equalization can be caused by many things. In most cases it is simply a case of not equalizing "early and often."
By early, I mean a week before you go on vacation (diving.) Once or twice a day - equalize your ears. Equalize on your way to the dive site, equalize while you wait to get in the water, equalize before you jump in, equalize on the surface before beginning your descent and equalize literally every two feet until you reach your maximum depth. This may sounf like overkill - but it works.
Another important factor in equalization is being properly hydrated. There are two things you should do before every dive. 1. Drink a bottle of water and 2. Eat a Banana. The hydration is critically important for a number of reasons and the banana provides potassium which greatly decreases the likelihood of cramping (legs/calves etc...)
It is also important not to over-equalize / forcefully equalize. Holding the nose and blowing is the most commonly used method. This method should include a slow, easy and methodical gentle blow... not a fast or fast / hard or sudden blow. A sudden blast of air into the eustation tubes can do more harm than good.
Now lets assume you're hydrated and have done as suggested above, yet you still have trouble with one or both ears as you descend...Try a different clearly method (swallow hard or wiggle the jaw or some combination of the two.
If nothing works... you most likely have an "issue." Issues may be simple congestion caused by colds or alergies. In these cases DO NOT TAKE A DECONGESTENT like Sudafed. Lots of divers do it... and many pay a hard price. I believe (with no stats to back it up - only theory) that many divers drown due to decongestents taken during diving. I'll explain a little further down.
If you are having pain during descent, you've waited to long to begin equalizing. If you've equalized as I suggested above and you still have pain, you have an issue. The issue may be a cold or allergy as already suggested or it may be something more. If the problem is always on one side, you may have a narrower or poorly functioning eustation tube on that side, you may have a blockage - such as polyps in your sinuses on that side, a deviated septum, ear infection or various other issues... some as simple as wax build-up on that side.
If the problem is with both ears it is most likely congestion or a sinus infection.
In any event, if you're following the rules and still having problems, it is best to consult an ENT (Ear, Nose & Throat) doctor and preferably one with diving knowledge. I speak from experience. I ended up having a deviated septum fixed and polyps removed and I still deal with a narrow eustation tube on the right side. After the sinus surgery my issues have been much improved.
Now to clarify my stance on decongestents in diving. Early in my diving career I had two very bad cases of reverse blocks which led to very serious bouts of vertigo at depth. In either case, had the regulator slipped out of my mouth - it is highly likely I would have drowned. The spinning sensation of the vertigo is likely to have made something as simple as finding my regulator and placing it back in my mouth - impossible. I consulted a DAN recommended physician who asked if I had taken decongestents before these occurrences. The answer was yes - because I was having trouble clearing due to congestion. He advised me that decongestents should not be used for diving - because if the medication wears off during the dive - the reverse block it can cause will be extremely dangerous - leading to a severe case of vertigo. I wish I had known this before I took the sudafed. To be honest, I consider myself more lucky to be alive today than good.
I did some reading and research and every year divers deaths are ruled drownings. In many cases there is no other ruling and in many of these cases, divers are found with air still remaining in their tanks. Medical examiners don't know enough about diving to ask the right questions. In these cases where no other cause of death is found - other than drowning... in other words, no heart attack, no anuerism etc.. the first question that should be asked is - was this diver taking a decongestent. You see, vertigo is not going to show up in an autopsy. Once the pressure escapes the ear, there is no sign of this as a cause - unless the pressure was such that during a too fast ascent - it literally ruptures the membrane...but to my knowledge, medical examiners are not checking the ear for cause of death.
It was suggested by my DAN ENT that this is a plausile explanation for otherwise undetermined drowning scuba deaths... and it should be looked at much more seriously by the industry.
I hope that I have helped you and helped to answer your question... and I hope you ge it straightened out...