A summation of my observations
This is not scientific as it relies on my memory and not on good data collection from a control group and an experimental group. These observations may help narrow where the problem is occurring however. It is meant to try and Identify Problem.
The rebound: When a script moves from low ci to high ci in its attempt to determine the point value of its newly altered state, it does not wiggle out to as high of a score that it used to. Therefore it rejects its latest altered state more often then it used to. This causes it to score less frequently or not at all.
The wiggle all function is not wiggling out to its full potential. There are 2 components to wiggle all: wiggle side chains and wiggle backbone. It appears that this is a problem with the wiggle side chains component (see 3.).
Wiggle side chains function is performing in a chaotic manner and often times it "sticks" and does not wiggle out sidechains. At this point it appears that the wiggle backbone function is able to cause an unusually large point increase.
It appears that there are two "areas" of coding that need to be examined. The first area is in sidechains calculations where the "wiggle sidechains" function is used, and an error perhaps caused by the new sliders.
The second area is more difficult to articulate, but could be easily overlooked. This area looks at the setup of the protein itself. It appears that the proteins are behaving in a similar way to folding at low ci techniques even when being played at maximum ci. In this case perhaps the problem would occur regardless of what client is used. Yet different clients would get different results because the protein is responding in an unstable manner to the lower ci.