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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.
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