Navigation issues, works through 1 menu, doesn't work through VM menus

[csimmo]

Hi. On the website I am building, I am having massive issues with what seems to be the SEO.
http://www2.abtsystems.com.au/
If you use the top menu, wait for the drop down and choose the category, it works perfect.
If you click the top menu (such as PC components) then choose the sub category, wether in the menu or from an icon, the url has the category ID and a re-enter of the main category (so its there twice).
If I turn SEO off, it makes no difference.
If I turn off product and category ID's and SEO, it blend my 2 test items that are in completely different categories together.

Can anyone explain why this is happening? I have spent money on the template and the accordion menu, and so far about 40 hours on this site, but this issue is a real killer!!

Oh, an update, the top menu uses the menu item VirtueMart Categories layout. Works perfect. The accordion menu and sub categories icons us the Categories layout. Why are there 2, and why has everything defaulted to the broken menu type? and how do I get it to choose the correct one?