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infection in molar

I have an infection in the root of a molar that's already a ton of work (4 surface fillings.)  Last November, I was going through stress, ground my teeth in my sleep and did some damage to the tooth which started the infection.  I went to my dentist and periodontist she referred me to.  Dentist made a nightguard, which I wear and she and the perio felt that the tooth wasn't loose in any way so they tried to save the tooth vs. do an extraction.  Dentist did a crown lengthening procedure in January and I did repeated check-ups with no sign of further infection.  
Then, a few weeks ago, the infection appeared again. She cleaned out the surface gums, took an xray which showed some "activity" near the root.  Again, I went to the perio for 2nd opinion and he and dentist both felt that, once again, the tooth felt stable so it was worth it to fight for the tooth vs do an extraction (I'm happy about this, btw.)  So she started a root canal yesterday, drilled a hole to let the pus drain out, put me on antibiotics and will finish the root canal early next week (or in two days, if someone cancels an appt--she's pretty booked.)  They (dentist and perio) feel she should do the root canal, but not put on a crown for sixth months, just do a temp crown and monitor the tooth.  If there's no infection after six months, then put on the crown.  If there is more infection, then extract the tooth.

My question:  after doing antibiotics and a root canal, why would an infection appear again? What triggers it?  Is there anything I can do to help prevent this type of infection (I use a waterpik and electric toothbrush twice daily.)
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The root canal may solve the problem of the infection in the root.  But if there's a fracture or other cause of the infection that the root canal does not solve, then its likely that a crown would not fix it either and thus a crown would be a waste of time for treatment.  

There's nothing you can really do to prevent it if there's a source of infection below the exposed surface of the tooth.  I would recommend being diligent about cleaning your teeth and maintaining your hygiene.
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