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First, I assume your fifth line should read catkin_init_workspace instead of catkin_make. I believe your issue is likely related to the cache used by rospack. Quoting from the rospack docs:

rospack re-parses the manifest.xml files and rebuilds the dependency tree on each execution. However, it maintains a cache of package directories in ROS_ROOT/.rospack_cache. This cache is updated whenever there is a cache miss, or when the cache is 60 seconds old. You can change this timeout by setting the environment variable ROS_CACHE_TIMEOUT, in seconds. Set it to 0.0 to force a cache rebuild on every invocation of rospack.

I have encountered exactly the same sort of behaviour that you are reporting in the past, and I've always understood this behavior to simply mean that the rospack cache is out of date. Running the command rospack profile will force rospack to re-crawl your active workspaces and refresh the cache. This page also supports my theory. Hope this info helps.