Sorry - but I still think there is something wrong here.
I have now regressed all the way back to the 2.0 install and I am still getting the PHP Notice errors.
To make doubly sure I made a completely new/fresh 2.0 install with no changes other than to switch on "Report all PHP errors" and "smarty notice reporting" plus I removed the assistent module to declutter the menus. This clean 2.0 install gives all the "Undefined index" errors - you can see this at http://www.tw2.enmoreservices.com/tikiwiki-2.0/ and login with admin/admintest to see the errors. I'll leave this test site open for a while so it is available for anyone to look at.
I then created a second clean 2.0 install which I upgraded to 2.1 by the simple "copy and replace" method - but this gives the same "Undefined index" errors plus when you clear the cache this triggers the missing tiki-2.1-mysql.sql error. You can see this 2.1 site at http://www.tw21.enmoreservices.com/tikiwiki-2.1/ and login with admin/admintest to see the errors. I'll also leave this test site open for a while so it is available for anyone to look at.
So I think there are bugs here - which whilst they don't seem to affect the running of my site are quite disconcerting.
Can anyone else repeat this?
Should I post this at the Bug list?