First, I'll assume you have already checked carefully that the water is not seeping down from the shutoff valve, or a tank to bowl connection.
As for the flange, short of raising up the flange....probably not an option at this point, I would choose flange spacers as opposed to what sound like would be an inch and a half of wax. Use about 3 to 4 spacers as necessary to get above the finished floor. Each spacer should be sealed in between with silicone, as well as the first spacer to the flange. These should be snugged up with long flange bolts and a nut on top.
One toilet with a hidden crack is not unheard of. Two...well what are the odds!
We have to ask the usual question, and don't take offense. If you have read the forum when this problem comes up we always have to ask:
Are you sure someone in the house ( young boy, older gent ) does not have bad aim?? Just have to eliminate all possiblities
Otherwise, this is one of those mysteries, so far.