sounds kinda bland but how are your trans fluid levels? My 2000 sr5 was doing this a little bit and I was a TINY bit low and it really has slowed way down..
diff fluid levels might have something to do with it as well, just a thought.. when i swapped my diff fluid i was a little short for about 2 hours then i filled it up, the fluid is so thick brand new, but when it warms up and gets beat up it really loses some viscosity it seems maybe that's incorrect.
My 2001 TRD does this also, Doesnt seem to evey time thought. I can't quite seem to pin it down. Ive checked the fluid a million times it seems. I changed the fluid shortly after I got the truck so I'm unsure if it did it before I changed it out.