If you are not harvesting yeast, even at the 5 gallon level, your missing out.
Yes, but I'd add the caveat: harvest and reuse yeast *fresh*. You can get away with storing it in the fridge, but even after only a couple of weeks you might want to make a starter. Or you may have no problems using yeast slurry older than that, but there's no guarantee. At the 5 or 10 gallon homebrew level, yeast is cheap, so the benefits are smaller. I personally like to make so many different styles that unless I know I'm making a string of american ales or german lagers, I'm not going to bother saving yeast. It is a great idea to plan a few beers in a row where you can reuse the yeast immediately and go from weaker to stronger beer... like Keith said, plan it so you make a high gravity beer after using a smaller beer to propagate. However, I'm not always this organized (or patient).
Which brings me back to the OP: when did you harvest the yeast? This sounds like a yeast health problem. The cone of a conical get get hotter than the rest of the beer, especially if it's not cooled, and the longer beer sits on it, the less healthy it is. If you follow Keith's advice, you should be good to go.
Edit: yes, this sounds like the issue. You probably pitched unhealthy yeast, and without aerating growth of new yeast was further inhibited.
We probably collected the yeast too late as the beer had been sitting on it for about 3 weeks when we collected it.