I've found that the encounter builder is usually fine, but I would spend lots of extra time setting up encounters using it only to find that the things I plucked haphazardly were only about, say, 20% less balanced on average.

At the end of the day it became a question on if it was worth it to run every encounter through that for being only marginally better than just grabbing and going. For some, they have the time to spare and it is worth it, and that's perfectly great! For myself I found that the extra variance just made things interesting and that 20% extra imbalance could be made up by the odd sneaky adjustment on the fly if I was ridiculously off base in where I expected the fight to end up in difficulty.