That's curious, then. I process in trays and don't have this problem.
What is your agitation method? I usually agitate by shuffling the stack either every thirty seconds or every minute, depending on the film/developer combination. I also turn the sheets 90-degrees periodically. I don't rock the trays when doing multiple sheets.
If I'm doing one sheet, I will rock the tray, lifting one edge, following the same interval as if I were using the method of shuffling, but I will turn the sheet 90-degrees periodically as well. I suppose I could remove the sheet and replace it, as if I were shuffling, but I figure the less I handle the neg the better.
Do you presoak? If not, that may be worth a try as well.