Here is what I did.
I didn't know for sure what you meant by the 'main' ini file so I deleted the one in the main directory 'mameui.ini
Started the program and it did the popup thing but recreated the file.
Then I searched the Mame directory for all .ini files and notice a folder called 'folders'. In here were 2 .ini files 'controls' and 'drivers' like mentioned in my popups.
I deleted or rather just moved them out of the Mame directory and it booted up fine without the popups.
I played a couple of games and they worked fine.
However, Mame did not recreate these 2 files....I search and they are nowhere in the Mame folder tree.
Is this in issue? It is working right without them but I would imagine they are there for a reason.....
Thanks for the help..