Hi, welcome to the forum.
I ran into similar issues when I moved up to the newer versions of Excel. The 'old' custom menu buttons that I had working in all my files were no longer supported.
Even if you say you're sunning both 2003 and 2013 on the same machine I think the different DLL files clash somewhere along the line.
In the end I just converted it all to custom ribbon menus.
I did however find a link once to open the old style command bars under the newer versions of Excel but do not remember which site it was, I think Ron de Bruin's site (which is an excellent site explaining the Custom UI (Ribbon)