There are only two ways for me to track a new comments flag for you guys. Either I base it on the last time you viewed the My Skins page or I base it on the last time you actually viewed the skin.
I considered doing it based on the My Skins page, however, this means if you were to page through your results or reload the page before going and looking at the skins that said they had new comments on them it would count those comments as 'viewed' and say you have no new comments. Also you would still have to at least page through all the pages of your my skins list to get this info updated. If people would really prefer this I supposed I could convert the system over for this. Basing it on the last skin view will give more accurate/real data.
No matter how its implemented it wont be able to save your comment number history if you clear your cookies.
There has to be some other way of doing this. Having a cookie to track comments kept on a users local PC is just not going to work. If they clear there cookies they have to re-initiate one for each of their submissions? Over and over again? Or if they want to check the site from a different computer, they have to create cookies on it to track their comments? Come on now, maybe try talking to other programmers, there has to be another way. I know my site and vStyler's (I maintain both), track new comments, forum posts, everything. It tracks it in a different way, but maybe if you talk to someone over at e107.org they might be able to help you out with some coding changes. The way of talking about doing it is just not going to work at all. All you will have is a lot of complaining users.