Pageant supports the same -restrict-acl option as the other PuTTY utilities to lock down the Pageant process's access control; see section 3.11.3.28 for why you might want to do this.
By default, if Pageant is started with -restrict-acl, it won't pass this to any PuTTY sessions started from its System Tray submenu. Use -restrict-putty-acl to change this. (Again, see section 3.11.3.28 for details.)