Baxter, I have processed quite a lot of 4x5 in Jobo reels and found that if I do 6 sheets on a reel, one sheet out of the six seemed to have uneven development. I first noticed this problem with vast expanses of one colour, like a sky or painted wall.
This was with C41, which is a shorter process, exactly ½ the time of E6. That may have had something to do with it, maybe. However, I found that by doing only 4 sheets on a reel I haven't had any more uneven development, in the last 10 years or so.
I use the outer and inner slots for all processing.
Are you using the film loader to help load the reels easily? If not, I suggest you think about it, it makes loading, a no fingers on the sheets situation.
Just remember to memorise the amount of clicks, as you turn the reel around!
Mick.