Shuffling is the most common form of agitation when using trays. Think of the film stacked up like a deck of cards one on top of the next. You grab the film in one hand and use the other to slide the bottom neg out and then gently lay it on the top. I shoot until I have 6-8 negs to do at once.
How are you agitating? This may be the reason for the uneven development.
For comparison--I use 1000mL of developer in an 8x10 tray for my 5x7 negatives.