subfloor damage near shower

We decided to rip up the crappy tile job in the master bath in our 9 year old house and discovered rotted subfloor next to and under the shower pan. The shower pan does not appear to have any holes. Attached by caulk to the shower pan is the bottom track for the shower door. When we removed it a bunch of water came out even though the shower hasn't been used for a week. Although the shower pan and door seem decently designed, our guess is that the mistake was to caulk the inside where the bottom track attaches to the shower pan. If that area had not been caulked, any water that somehow got under the door track would have been able to run down into the pan. Instead, 24 hours a day, a bit of moisture, invisible to us, was moving from underneath the door track to the floor of the master bath.
You might want to see how your shower door bottom track is attached to your shower pan. If caulked on the inside, consider removing the caulk or at least creating a few weep holes.
We have a 1 foot diameter or rotted subfloor to fix because of this problem. All of the walls around the shower have been stripped to the studs and there is no other indication of a leak. The only possibility is the shower door installation.
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