Navigation pane not showing in merged output on server (IE9)

RH10 | WebHelp

We've moved our WebHelp outputs from an externally maintained server to an in-house server, but the left-hand navigation pane isn't displaying in our merged Help system. In our user guide (which isn't merged) the pane displays fine, but in our release notes (which is a merged system) it doesn't want to show itself. The main navigation pane and topic pane are fine, it's just the left-hand navigation pane that's blank.

I'm running IE9, but the weird thing is that it displays correctly in Firefox. It also works when run locally.

Both Help systems worked absolutely fine on the previous server, so I'm wondering if there's a conflict with something else that's running on the new server (e.g. our website's CMS, etc.) or whether it's a permissions thing?

My issue seems similar to other posts on here, but I'm using IE9 not IE11.

I'd be grateful for any ideas.

Thanks

Jonathan