I've heard E6 can ruin C41. Most labs will run cross processing at the end of the day before they dump the chemicals. So I'm told.

It's likely your chemistry was fine after cross processing, but that whatever is in the E6 catalyzed some sort of decomposition of your developer (oxidation?) and that after being left a while it got to the point it was no good anymore. That would be my guess, but I don't know a thing about E6 chemistry so hopefully someone else can come along and shed a little light on it for us.