After much research it appears this is an issue with all sites that use flyout menus.
I ended up using wayfinder to display the top menu and first drop down and then the "hasChildren" snippet to check for children. If there are, it displays them as links in a side menu with wayfinder, if not it shows a link back to the parent page.
Below are the chunks and snippets I used to do it. Nothing special, but may save someone else having to figure it out.
Top Menu:
[[Wayfinder? &startId=`1` &level=`2` &titleOfLinks=`longtitle` &parentRowTpl=`cssplay_revParentRow`]]
Chunk to check for children:
[[hasChildren? &noChildChunk=`SideParent` &childChunk=`SideWayfinder`]]
SideParent chunk:
[!Wayfinder? &startId=`[*id*]` &level=`1` &displayStart=`true` &titleOfLinks=`longtitle` &parentRowTpl=`cssplay_revParentRow` !]
SideWayfinder chunk:
<h4>[*menutitle*]</h4>
<ul><li><a href="http://www.emanz.ac.nz/[!GetField? &parent=`1` &parentLevel=`1` &field=`alias`!].html" title="">[!GetField? &parent=`1` &parentLevel=`1` &field=`menutitle`!]</a></li></ul>