Chris,
I had similar problems when developing sheets in trays emulsion-side down. It seems the ribs on the bottom of the tray caused uneven developer flow and some obvious increases in density around the rib areas. I tried emulsion side down since I heard it minimized the risk of damage. Unfortunately, it didn't work nearly as well as emulsion-side up; I switched back after one session! If you are developing emulsion-side down this may be your problem. (BTW, by just training myself to be alert and careful, I have virtually eliminated negative damage from handling. My last batch of 150 negs came out flawlessly except one neg that I damaged by dropping a funnel into the film washer during washing. I've now moved the film washer away from under the shelf...)
I also shuffle from bottom to top, (emulsion-side up) so that the moved neg gets a bath in a lot of developer, not just the little bit under the stack. Maybe shuffling in this manner would help too. Having the full depth of the developer above the exposed emulsion side of the negative has to help with evenness.
I also make sure that each sheet gets adequate developer when initially immersing them. After the water pre-soak (also indispensable if you want to minimize blotching), I immerse the sheets over the period of 30 seconds (e.g., six sheets = one sheet immersed and agitated every 5 seconds).
My scheme is to go through the stack once every 30 seconds for the first half of the developing time, then slow to once per minute at the halfway point. I turn the stack 180° each time through for the first half and switch to turning each sheet as I shuffle it for the slower shuffling. I time the shuffling so that I don't have a pause at the end (e.g., six sheets = one shuffle every 5 sec. for the first half, every 10 sec. for the second half of development).
When shuffling, I very gently immerse the sheet pulled from the bottom to minimize turbulence around the edges of the negative. Just a nice, easy float to the bottom aided by a little finger pressure.
I finish with sheet one on the bottom, pick up the entire stack, fan it like a hand of cards with the bottom sheet sticking out on the right (I work from left to right) and then immerse the sheets in the stop bath in the same order and interval as I immersed them in the developer. This ensures exactly the same developing time.
I use PMK primarily, and have become rather obsessed with getting even development, since it is such a finicky developer in this regard. I've been using this scheme for a long time now and am quite pleased with the evenness of development. Maybe there are some tips here that will be of help to you.
Best and good luck,
Doremus Scudder
www.DoremusScudder.com