i had root canal work on a top cheek tooth about 2 years ago, and it began to hurt toward the end of last year. the dentist x-rayed it, and referred me to the dental hospital. there, they discovered that an infection had grown under the tooth and eaten a hole through the jaw into the sinuses. apparently this is not uncommon, and is because there are sometimes root branches that even the best dentist can't get to, this is the seat of the infection. it's treatable, the dental surgeons drill through your jaw and fill the tooth root from underneath, and it's about 80% successful. so far I've had no more trouble, but it's left a hole in my jaw covered only by gum tissue - they warn you not to sneeze too hard, or it could rupture.
of course, your issue may not be like this - but be sure the dentist takes a good look...