• Consider a Matrix build of 2x3 (debug/release x 3-variants)
• add the doxygen generation build step "Generate documentation using Doxygen"
• add the doxygen publisher "Publish Doxygen"
• trigger a build
• see that each build-configuration does a doxygen run
• see that there's doxygen only published once on the "main index" of the matrix build

Possible solutions:

• run doxygen only once on the parent workspace of a matrix build and there fore publish only one doxygen documentation
• publsh all built doxygen documentations
• add a configuration filter for doxygen and publish all resulting documentations