In UI15, all applications are not visible in the filter navigator for a user.
This behavior can be caused if the user selected a 'perspective' which can limit the applications seen in the navigator for that user.
This is a user preference and it can be set by clicking on the downward arrow next to the Filter in the filter navigator and then selecting one of the values like Admin, ITIL, Reports, All.
The simplest way to fix this issue would be to choose the value All for the user preference, 'perspective'. (screenshot below explains how to do this in the UI)