So, I have installed and created my apps and we are on to getting it to look right.
I activated the Custom Comment Template and saved changes with the default theme selected.
I then tried to change to the WPMU.org template and the changes do not display.
I tried it on another site but switched to WPMU.org template before saving changes and it now displays the comment form as on WPMU.org. If I try to change it to the default it continues to display the WPMU.org theme.
I tried clearing cache to no avail.
It would appear that once you select the theme that changing to another theme is not possible.
I tried deactivating the Custom Comment Template and reactivating it to no avail.
Any thoughts would be appreciated.