This conversation shows a lot about why "gas line sanitization" is just one of those things that I've never felt fully comfortable with. None of us works in a completely aseptic environment, so admittedly there is always some
level of contamination in homebrew (and probably all beer if we're talking about counting cells). The trick seems to be keeping the unwanted organisms to a minimum.
With that said, the best way I can think about it is that:
- "The front end" of yeast propagation is the most dangerous place for contamination, as you will grow most unwanted organisms right along with your yeast (this is why I worry about the inside of the oxygenation tubing as I sometimes oxygenate starters before putting them on the stir plate)
- "The front end" of fermentation seems like the next big danger area, as you're preparing for another growth phase and dumping your microbes into an all you can eat buffet (this is why I worry about the inside of the oxygenation tubing)
- Packaging seems less concerning than the rest of these environments as the conditions for multiplication inside packaged beer aren't as favorable as the other environments; However, anyone who has ever seen a gusher knows it's still quite possible to screw this up
Bringing it back to the OP's question, it seems like we've had several people convinced that dirty gas lines on the beer gun could be the cause of their issues. This seems plausible to me, but applying Occam's Razor it seems like a gas line at packaging is the least likely place to go looking for a contamination source unless you've thoroughly eliminated the more likely possibilities first.
As for whether I will run sanitizer through the inside of my oxygenation line after all this -- probably not. I leave it connected to the tank and clean/sanitize the wand and outside of the line already. It seems like pulling it apart might create more opportunities for contamination than leaving it alone (unless I somehow managed to get beer inside the line, in which case I'd just buy new tubing and start over).