After taking a quick glance at your notebook, it looks like the issue is introduced when your Plot's Epilog option is trying to show graphics that rely on the variable that Plot is localizing. The following is a simpler example which demonstrates the same issue:
Manipulate[
Plot[Sin[x], {x, 0, 10},
Epilog -> ReleaseHold[Point[{x, Sin[x]}]]], {x, 0, 10}]
If needed, this can be worked around by using a different variable for your Epilog plotting than for your Plot, for example a simple fix that you can implement could be something like:
Manipulate[a = x;
Plot[Sin[x], {x, 0, 10}, Epilog -> Point[{a, Sin[a]}]], {x, 0, 10}]
This did seem to work well in earlier versions, so I'll report the regression.
Kyle