@Peter: thanks for the feedback, here are my answers to your comments:
1. I replaced "&" with "&" and get the following error which is
probably why I had "&" from when the app was first built.
ERROR
Exception occurred parsing base config file 'C:\Inetpub\wwwroot\project
\configs\mach-ii.xml' for module ''.
Type: Expression || Message: An error occured while Parsing an XML
document. || Detail: The entity name must immediately follow the '&'
in the entity reference. || Original Template: C:\Inetpub\wwwroot
\MachII_1-8-0_RC1\MachII\framework\AppFactory.cfc at line 133
2. I did have the urlParseSES property set to true. I don't want
"index.cfm" in my URLs because I want my URLs to appear as if it was a
flat website i.e. /folder/folder/page.htm. I guess you could argue
that /index.cfm/ is the 1st folder however I just don't like having it
there, plus I feel it degrades SEO because the spider would see
content as being an extra folder deep in the app so less relevant.
3. I don't have a urlBase property set. But I have run into the
problem you speak of with parameters being piled up on each other. Now
I always use absolute urls i.e. "/..."
As mentioned above I have found a fix so don't waste your time
investigating for my benefit however I'm happy to keep digging if you
think this is a bug or upgrade querk.
Cheers
Matthew