Custom template not copying to cloned store

I am using version 1.3.8a and have had an existing store with a custom template and have just made a
clone of the store.

I just installed a new store using Fantastico. I then copied the existing database into the new db.

So now I have a cloned store (on the same server, just different folder name and copy of mysql db)

I then copied all the files from the original store into the clone store folder except includes/configure.php and admin/includes/configure.php

But my custom template is not working properly. It shows that it is installed in admin but is a mess to look at,
images not showing and all sorts of strange colours etc.

So my question is, what is the most likely reason for this? I thought I did the clone procedure correctly, everything seems to work it just looks horrid.

Does it sound like something didn't get copied or conversely that something got over-written that shouldn't have?

OK, I solved my own problem.

It was a matter of some key template files not getting copied over. When they were downloaded via ftp somehow the folders are there but they were empty (not all, just a few folders that happen to have the images etc.).

It's just one of those unexplained things that happens with shuttling data around.