I had a similar issue when using the pose editor on jpj. I start off creating a pose interpolator on frame 1 where all axis are set to 0. I then create a pose on the next keyframe but instead of weighting the new pose as 1 it instead weights it as 0.5. How I got around it with jpj was by using a different deformation order other than automatic, which didn't work in the same way. I'm not sure if it is an issue with my computer or copy of maya as I had the exact same issue before, but my version of maya has been updated to the latest so the issue isn't down to an old version. I wasn't able to make it into uni today but will be in tomorrow to try it on the computers in university, as I have a feeling that may be the problem, but at the moment I can't find any fixes for this issue online.
I've spent a lot of time trying to correct the skinning and think I've got it to a point where I can start using the pose editor. There isn't a whole lot of movement capability of the main body but I think this is fine as it is still capable of having as much movement as I would like out of it.
I think I've got the painted weights as good as I can get for the legs. There are still issues, mainly in the back of the leg which will have to be corrected using the pose editor.
I've added weights to the leg for the hip, knee, ankle and foot ball joints. I know for sure I'm going to have to use the pose editor to fix the issues in the back of the leg when bending back as I don't think it is fixable with just the paint weights tool. Another issue I'm unsure about is that the joints orient on different axis despite all going in the same axis relative to the world. I'm not sure if this is a problem from the way in which i created the joints or if it is not an issue at all.
Knee Joint:
Bend forward - Y, -20
Bend back - Y, 20
Ankle Joint:
Bend down - X, 20
Bend up - X, -15
Foot Ball Joint:
Bend down - Z, -40
Bend up - Z, 20
I haven't been able to finish this tutorial as the file has become too complicated for my pc to handle and keeps crashing. I am up to blending the elbow. I will have to continue it on a computer at uni tomorrow.
EDIT: Finished