Sorry I got my measurements incorrect (wired the module wrong when I went to take a photo and check voltage). SDA is 0.198V and SCL is 3.3V with 3 modules plugged in and adafruit vl53l0x sketch uploaded. Ran the sketch again with the same results. Each one works individually and 2 at a time, but not 3. I also tried swapping out one of the modules for another one with the same outcome.
The wire configurations are exactly the same when changing out the Due. I have tried multiple sets of jumpers and breadboards thinking that something might have been broken. It didn't solve the problem, unfortunately.
Voltages when running the empty sketch with I2C bus enabled:
No sensors: SDA=3.273V; SCL=3.273V
Sensor 1 connected: SDA=3.273V; SCL=3.273V
Sensor 2 connected: SDA=3.273V; SCL=3.273V
Sensor 3 connected: SDA=3.273V; SCL=3.273V
Sensor 1 & 2 connected: SDA=3.273V; SCL=3.273V
Sensor 1 & 3 connected: SDA=3.273V; SCL=3.273V
Sensor 2 & 3 connected: SDA=3.273V; SCL=3.273V
All 3 sensors connected: SDA=3.273V; SCL=3.273V