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It turns out this was happening because the component libraries had the same name even though they were in different paths. I was still using the default name for the libraries in each CMakeLists.txt file, ie:

pkg_one/CMakeLists.txt:

...
orocos_component(components src_1.cpp src_2.cpp)
...

pkg_two/CMakeLists.txt:

...
orocos_component(components src_3.cpp src_4.cpp)
...

So giving these unique names solved the problem.