Same template filename in multiple directories in path

I'm sure I should know the answer to this, but I can't find it:

I have multiple directories in my template path, which will vary on
multiple calls to my script, but there's always a default template
directory. All of them contain a file "index.tpl", so depending on the
template path for any given call to my script I will be targetting a
different index.tpl.

It seems [*] that they all compile to the same file in templates_c, so I
generally get the last compiled version of the wrong template.

How do I fix this?

[*] I'm debugging this remotely and that's the conclusion I've reached;
the site is currently using v2.6.3. If an upgrade will fix it or this
just shouldn't be happening anyway I'll look for other problems in my code.

-- 
Mark Rogers
More Solutions Ltd