I have seen this when using my Diatom Filter for extended periods of time (Vortex says it can be used as a permanent filter; I tend to disagree...). What you're seeing is a rust-colored algae growth, and I assume this is happening because of the proportionately higher amount of nutrients that touch the inside of the tubing of your filter. I tried to scrrub mine out, but have no pipe cleaner long enough. Instead, I just ran water through the hose, and vigorously clenched the hose at 1-inch intervals, rubbing the upper and lower surfaces of the inside of the hose together. This, along with the high water pressure, was enough to get most of the gunk out.
I wonder if other canister filter ppl have this issue, and if all canister filter intake/outflow tubes are translucent like James's. Perhaps others aren't aware of this happening.
I can't see this blocking up your tubes, and this is certainly not the *cause* of your green water, but it may be symptomatic of over-feeding. How often do you change your water? You might want to think of changing water a bit more frequently and testing for nitrate and phosphate levels. Light reduction will do nothing for rust algae (as is obvious.... yours is in a dark place), so you may *not* benefit from shutting the tank lights off for a while...
So, keep your water as clean as possible and starve those nasty algae!