The PPU can get that way fast if you have not been running a quality full synthetic before. According to the cw, it will clean faster than almost anything, including HDEO. I was doing 5k changes on dino, and it came out carmel-colored. The I switched to PP (not the ultra, but very similar) and it was dark in less than 1k miles from the cleaning action. After a few OCIs this will taper off as it gets clean and stays clean.
On the ATF, I really don't like doing whole flushes at that interval. A drain/fill every 30k keeps the fluid refreshed and performance from suffering. Like you, I notice that if you do a drop test (take out the dipstick, put a drop of ATF on paper) it can look red, but then when you drain or pump it, it looks black from the suspended particles you can't see on the stick/drop test.
Now: '94 GS300, '02 ES300
Past: '02 Solara, '98 Land Cruiser
Other: '98 Acura SLX, '91 Audi V8/5 speed
Past: too many BMWs to be bothered with any more.
Un-wheeled: '98 Peruvian Paso