Spiral Tank Processing

[mosesfilm]

I have some questions regarding at home Spiral Tank processing. I have been mixing 2 litres of chemistry for 100' rolls of color reversal(ORWO/Svema & Kodak E-6) and, just recently, color negative(ECN-2) 16mm film. After running the first devloper, the solution is sometimes black and seems to effect the image of the bottom 50' layer of film (dark and muddy). Should I only run 50' at a time at the top spiral?Is this remjet? (Svema & ORWO do not have remjet.) Should agitation be constant to mix chemistry, or maybe try to filter the developer before running the other 50'? You advice would be greatly appreciated.

Thanks