It seems like the behaviour is reproducible. On the include lines with the path missing nothing is displayed in the VA definition field. But Alt+G works on the type name within the code and opens the correct file. But Alt+G on the include line doesn't work.
Meanwhile I was able to fix this part of the problem. I had switched off the "Parse all files when opening a project" option because we have a huge code base and it takes a while to scan every time I open a solution. I switched it on again and did "clear" and "rebuild" too. Now VA finds the include files again.
Only the first problem with the relative paths persists. It seems that for some projects VA uses relative paths from the current file like #include "../../xmlhistory/globexport/historyelement.hpp"
and for others relative paths from the %INCLUDE%-path, like #include "base/z96util/globexport/map.hpp".
But within the same project it has always the same reproducible behavior.