Debian Wheezy, also referred to, I think, as Raspbian. All cards have had the OS created by the same process. I hadn't heard of checkinstall. Thanks - I'll investigate.
Update: I don't think checkinstall is going to help me, although I'll bear it in mind. The problem is that there's something - a file, some hidden variable or something else - that I'm not copying and that therefore I don't know how to put into checkinstall. If I knew what to copy, I can imagine situations where it might help. At the moment, I just want to know what it is I'm failing to copy.