First of all, from the time I deployed IBM Connection navigation bar (this one that lists the applications: home, profiles, blogs and etc.) worked correctly. But some time ago it started to go away(hide) when I switch to Profiles or Files apps. In all the other applications it is working like a charm(visible).
So, possible correlation:
Any tips on how to resolve the problem?
After some time I've discovered that the problem was with customization of headers and footers of applications (Profile and Files apps). While integrating to WebSphere Portal there were made changes to footer.jsp and header.jsp with wrong values.
In whole, there are two ways to customize look and feel of IBM Connections:
Fore more information refer to documentation.