Luis Benitez published usefull article about how to make work Lotus Connections portlets through WebSeal: http://www.lbenitez.com/2010/05/getting-lotus-connections-portlet-to.html
As far as I understand, this problem appears only if WebSeal is placed between Portal and Connections. If Portal and Connections communicate directly (ok, may be through HTTP,proxy or load ballancers), that LTPA should work and no modifications will be needed. But this is my assumption, need to check it.
Grate article about how to make Lotus Connections portlets work through WebSeal