What would cause proteins to get stuck in the stacking layer of a SDS-Page gel
At the interface of the stack gel and resolving gel is a pH change and a change in gel density.  If you feel certain that your protein is not crosslinking so much that it can not enter the gel than I would think about the pH of the sample and the effect of Cu ions on the stacking effect of the stacingk gel.  Is your sample the normal blue color (indication of pH) when you load it (compared to other samples you load)?  Are you overloading the gel?  I have seen overloading cause the effect you describe because the proteins get concentrated to a very high degree before entering the resolving gel.  Could the Cu ions be affecting stacking itself?  

Read http://en.wikipedia.org/wiki/SDS-PAGE.  Specifically the section on buffer systems.  You might want to try a different buffer system.

Finally, you could try an acetone precipitation to try to remove the Cu ions and other chemical and see if that helps.