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:
- change look and feel for all applications (jsp files in folder *%connections_install_dir%\data\shared\customization\%app_name%\nav\templates*)
- change look and feel for every application\feature (every .war file has nav directory that contains the look and feel information)
Fore more information refer to documentation.