Sometimes while swapping to certain themes I get a message saying that
"Uninitialised module
*popup "module docs" -------- "
Is this something to do with the theme not being OTS? Is there a line that should be added to the themes step.rc file? Is it something to do with my OTS setup?

Can anyone help me with this problem?

from what you've written there, it looks like syntax... $module docs$ should look like that and without the quotes... and you should make sure that your step.rc points this to the right folder... otherwise check the popup2 doc (or whatever popup module you use).