This is what happened:
# for i in $(seq 10) ; do sem -j 2 "echo $i started ; sleep 2; echo $i finished" & done
[1] 96842
[2] 96843
[3] 96844
[4] 96845
[5] 96846
[6] 96847
[7] 96848
[8] 96849
[9] 96850
[10] 96851
parallel: This should not happen. You have found a bug.
* The version number: 20130922
* The bugid: write_idfile: $HOME/.parallel/semaphores/id-2fdev2fpts2f43/id-2fdev2fpts2f43
* The command line being run
* The files being read (put the files on a webserver if they are big)
If you get the error on smaller/fewer files, please include those instead.
After that, the jobs (except for #4) all ran as expected.
The file mentioned ($HOME/.parallel/semaphores/id-2fdev2fpts2f43/id-2fdev2fpts2f43) did not exist when I looked. (The dir was empty).
Running the same command a few times does seem to repro the same failure.
Hope that's useful!