The only thing I can think of right now is that in the modified package they may have left the name and GUID for the original p&p package which should cause an error at installation time... but you're not getting any errors when installing the modified version of the package right? The modified package will install just fine but it will never show up in the Guidance Package Manager right?
If my assumptions are correct, let's check a few things in trying to determine what may be going wrong:
1) Take a look at your C:\Documents and Settings\All Users\Application Data\Microsoft\Recipe Framework\RecipeFramework.xml file and doublecheck that there is a <GuidancePackage> element corresponding to the modified package (its Name & Guid attribute should not be the same of the original package).
2) If 1) was true, use regedit to lookat HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VisualStudio\8.0\Packages there should be a subkey named after the GUID for the modified package.
Let me know about 1) & 2) and we'll try to work from there.
thanks,
-Victor.