Hi,
It's strange because FLEXIcontent is natively designed to work with JComments. It functions properly with all template providers but I don't know the Artisteers auto generated templates.
Which version of FLEXIcontent are you using?
Have you tried to disable css style from FLEXIcontent trough the component configuration?
Cheers,
Emmanuel.
PS: What is the issue exactely? Could you post a screenshot?
I use an artisteer-generated theme, FLEXicontent and JComments and all works fine (only Jcomments' latest module doesn't work, but this isn't the place to talk about this issue). So i guess it's not FLEXIcontent's fault...