Despite your dentist's best efforts to clean and seal a tooth, new infections might emerge after a root canal. Among the likely reasons for this include:
More than the normally anticipated number of root canals in a tooth (leaving one of them uncleaned)
An undetected crack in the root of a tooth
A defective or inadequate dental restoration that has allowed bacteria to get past the restoration into the inner aspects of the tooth and recontaminate the area
A breakdown of the inner sealing material over time, allowing bacteria to recontaminate the inner aspects of the tooth
Sometimes retreatment can be successful, other times endodontic surgery must be tried in order to save the tooth. The most common endodontic surgical procedure is an apicoectomy or root-end resection. This procedure relieves the inflammation or infection in the bony area around the end of your tooth that continues after endodontic treatment. In this procedure, the gum tissue is opened, the infected tissue is removed, and sometimes the very end of the root is removed. A small filling may be placed to seal the root canal.
It is difficult to point out the exact cause without actually looking at the tooth and a checking it, but it might be because of some long standing infection inside. Am sure your dentist must be trying his/her level best to treat it well. Sometimes if the pain does not subside even after the initial root canal steps the treatment needs to be modified. You can visit an Endodontist or a Root canal Specialist for a second opinion if you wish.