What you are describing sounds like "gas bubble disease" rather than popeye. Popeye is basically the entire eyeball swollen/enlarged, or pushed forward by a swelling behind it.
Gas bubble disease is diagnosed by the finding bubbles (air emboli) within the blood vessels, gills, and eyes of fish. One possible cause is the supersaturation of the water with any gas (nitrogen, oxygen, or carbon dioxide most commonly)--in other words more gas dissolved in the water than it normally holds.
What causes gas supersaturation of the water? Pump cavitation can do this. Do you have a closed loop on your tank? I have heard that this can be a problem with them, esp if the output diameter is too small.
Some heavily planted freshwater tanks have a problem with oxygen supersaturation.
Treatment? Moving the fish to a tank with normal levels of dissolved gases, while correcting the source of gas supersaturation.
Other factors may contribute to the foration of oxygen bubbles--what are your tank parameters? I found a reference that suggested that high temp and alkalinity can contribute to this problem. Do you have lots of microbubbles in your tank, esp ones that stick to surfaces?
