why did clFinish cause a shorter execution time for collaborative computing

What you are doing should work if only the thread that is running the FPGA kernel waits on clFinish(), and the total run time that you measure should be the run time of the slowest thread (which could be the FPGA or the CPU thread), rather than the sum of their run times. As fand suggested, can you tell us where your timing starts and ends?

initialize_opencl();
define_shared_opencl_event(event);
start_timing();
fork_threads();
if (thread_num == 1)
  execute_fpga_opencl_code(&event);
else
  execute cpu_cpp_code();
join_threads():
wait_on_opencl_event(event);
end_timing();