Muscle lets you reset the base pose for a muscle or bone, even if it is already skinned. This means that even after you start skinning, you can reposition or edit the default position of that object so that the Sticky weights skinning is effectively reset. See Reset base pose for selected Muscle Objects.
Make sure that when you bound your muscle the Sticky Bind distance was set large enough to include the points you are weighting for, or Re-Bind sticky for the muscle. See Re-Bind Sticky for selected Muscle Objects. Also, in the Influence list of the Muscle Paint window, make sure that the "HOLD" weights option is not enabled for any object that is also weighted to that point if you are trying to scale or smooth weights.
There is also a showWarnings option on the Muscle deformer that you can turn on to see which muscles may have points outside the range, so that you can re-bind sticky on those muscles. Points will no longer fly off, but the deformation may get slower as binding information is calculated ‘on the fly’ as needed. To fix this, see Auto-Fix invalid Sticky Bind points.
The Paint Weights for polygon object uses Maya's polyColorPerVertex node to help display coloring, so you will see this node on any polygon object deformed with the Muscle deformer. In addition, any earlier values are overwritten. If you are using the polyColorPerVertex node for your own purposes, you need to finish painting and setting up deformation weights first, before you go and use the node for your own purposes.
If you change from painting to use the Move or Rotate tool (for example), you have effectively exited the Paint mode. To return to painting without having to close and reopen the Muscle Paint window, reselect the object you are painting weights for, and in the Muscle Paint window, click on the bones/muscle or weight in the list of items you are painting.
