could not find absolute location of file in autotools subdirectory

Linux, autotools project with subdirectories.

None of the files in subdirectories open in the editor when double-clicking the project tree.

None of the files in subdirectories open in the editor when clicking build issues, "File not found inputeventreceiver.h", etc..

When build errors are found "Could not find absolute location of file "inputeventreceiver.h", etc is printed to the console.

Sample structure:

configure.ac

Makefile.am

src/Makefile.am

src/lib

src/lib/Makefile.am

src/lib/inputeventreceiver.cpp

src/lib/inputeventreceiver.h

No issues with the files in the root, but nothing below src is found. Right click "Open in editor" works, though.

4.2.1 used to suffer from this occasionally, but a restart always made it disappear. Not so in 4.3.0, unfortunately.