I don't see any major problem with using Response.Redirect other than you should be careful not to redirect more than once in a given request or it can negatively impact SEO.
Definitely I think the problem is related to Server.Transfer, and you should probably be using Response.Redirect instead unless you have a very specific reason to use Server.Transfer and understand the implications of using it. I don't think I'm using Server.Transfer anywhere in mojoPortal but I'm using Response.Redirect in lots of places. There is nothing intrinsically evil about redirecting, there are lots of good and appropriate uses for it in my opinion. Very commonly I will use it after post back processing in order to get out of postback so that refreshing the page can't make a duplicate postback. I also redirect to the access denied page if a user has no view permissions and there is various redirect logic for after login or registration or redirecting to the order details after an order is complete, etc, etc.
I'm certainly not aware of any ajax issue related to Response.Redirect as Slaven has suggested, other than you don't want to redirect inside an ajax postback, thats a bad idea and using Server.Transfer inside an ajax postback would also be bad.
Hope it helps,
Joe