I am looking into an issue where Tagalong markers are not taking over from default markers. It will be in an upcoming patch release for Tagalong later this month.
The icons and icon array should be working as expected. I spent most of today testing that system on a large client install and it all behaved properly with Tagalong 4.1.
Looking for faster forum responses? Check out the Premier Subscription. Premier forum questions are answered within 1 business day. Customer that purchased the Kitchen Sink or The Experience package can have the setup fee waived, ask for details.