These irregular clicking noises in the ear should NOT be confused with tinnitus. Rather, irregular clicking noises in the ear are almost always due to muscle spasms... just like "eye twitching" or "facial twitching". BUT, instead of being able to "see" the twitching as with eye twitching, one hears the twitching instead since the muscles are located around or in the ear.
1) Palatal Myoclonus
2) Tensor tympani muscle spasms
3) Stapedius muscle spasms
The first potential cause (palatal myoclonus) can be diagnosed by seeing "spasms" of the soft palate that occurs in time with the clicking. Spasms of the soft palate can be visualized by simply looking in the mouth or by nasal endoscopy. Click here to watch a video of these spasms.
The reason one is able to "hear" the twitching is because the muscles of the soft palate extend up into the ear via the eustachian tube.
Treatment of palatal myoclonus is by botox injections to the muscles that are twitching.
Just like botox treatment anywhere else in the body, the effects are only temporary and needs to be repeated every 3-6 months.
Regarding tensor tympani and stapedius muscle spasms... these muscle are not able to be visualized as they are located within the middle ear. The tensor tympani attaches to the malleus ossicle (the "hammer" of the 3 middle ear bones) and the stapedius muscle attaches to the stapes ossicle (the "stirrup").
|Image from Wikipedia|
Known as middle ear myoclonus, unfortunately there is no "test" once can obtain to diagnose this problem with absolute certainty. It is based purely on history and excluding palatal myoclonus as a diagnosis (no soft palate twitching seen even though the patient is able to hear it).
Even more unfortunately, the only way this problem can be definitively treated is surgical... the muscle gets cut. Botox can not be utilized as one needs to be able to "see" or "feel" the muscle in order to inject botox. This surgery is performed by a neuro-otologic surgeon.
See the full list of surgeons who can perform this surgery here.
There has been some anecdotal suggestion that certain supplements like Magnesium Oxide or muscle relaxant drugs like flexeril might help.
Read more about this problem here.