Are you letting the beer sit for any period of time before you start filling bottles? I used to have the same problem regularly despite many others here saying the swirling from racking is sufficient to mix it all evenly. I started to gently stir with a large sanitized spoon and have not had this issue anymore. If you decide to stir you do risk oxidation, but I personally have not experienced that yet. Sometimes the beers don't all carb up at the same time as well, so more time out of the fridge may be needed as well.
No yeast, no beer. No beer, no civilization. Therefore, we really have yeast to thank for all our modern-day conveniences and tasty beer
*Member: The HBT Sweaty Fat Guys Cigar club