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You don't seem to have a declared dependency between the task_executor target (created with add_executable) and the targets for generating the files with flex and bison. My guess is that running catkin_make -j1 ... would possibly work around the issue, and that adding a line like add_dependencies(task_executor lexer parser) would fix the problem for multi-threaded builds.

If that doesn't work, you mentioned that as a normal CMake package it worked. Could you post that CMake project? Can you try building that CMake project with make -j2 to see if you can reproduce the issue with the plain CMake project?

It seems to me that the most likely cause is that catkin_make defaults -jN where N is the number of cores on your computer, but you didn't do that when running cmake/make manually.

Hopefully that helps,