Mystery solved. As it turns out finding struvite crystals in the urine is totally natural and poses no threat to the dog except when there is also a bladder infection. So the struvite crystals do not cause the infection but the infection causes the crystals to form stones if left unattended.
It is very important to check your dog's urine once in a while and if there is an on-going problem then have your vet take a sample directly from the bladder to make sure it's actually the bladder that is infected. This is especially important in female dogs. Then put your dogs on a antibiotic for a period of time. Joy was on an antibiotic for three weeks and is now infection free.
There is no need to change the diet although I have started making dog food again. The dogs still have access to Acana in the evenings.