I installed everything on another Bela for testing (the other is in place in the installation). I could reproduce the issue. Here is the output:
root@bela:~# ls -l /proc/*/fd | grep -B10 tmp/fifo
ls: cannot access '/proc/20344/fd': No such file or directory
lrwx------ 1 root root 64 Mar 3 14:03 1 -> /dev/ttyGS0
lrwx------ 1 root root 64 Mar 3 14:03 2 -> /dev/ttyGS0
lr-x------ 1 root root 64 Mar 3 14:03 3 -> /etc/issue
/proc/4/fd:
total 0
/proc/414/fd:
total 0
lr-x------ 1 root root 64 Mar 3 14:07 0 -> /dev/null
l-wx------ 1 root root 64 Mar 3 14:07 1 -> /tmp/fifo
lrwx------ 1 root root 64 Mar 3 14:07 10 -> socket:[17983]
lrwx------ 1 root root 64 Mar 3 14:07 2 -> socket:[17983]
/proc/418/fd:
total 0
lr-x------ 1 root root 64 Mar 3 14:07 0 -> /dev/null
l-wx------ 1 root root 64 Mar 3 14:07 1 -> /tmp/fifo
--
lrwx------ 1 root root 64 Mar 3 14:07 44 -> /dev/rtdm/rtdm_pruss_irq_0
lrwx------ 1 root root 64 Mar 3 14:07 45 -> /dev/rtdm/rtdm_pruss_irq_0
lrwx------ 1 root root 64 Mar 3 14:07 5 -> /dev/i2c-2
lrwx------ 1 root root 64 Mar 3 14:07 6 -> /dev/i2c-2
lrwx------ 1 root root 64 Mar 3 14:07 7 -> /dev/i2c-2
lrwx------ 1 root root 64 Mar 3 14:07 8 -> /dev/mem
lrwx------ 1 root root 64 Mar 3 14:07 9 -> /dev/i2c-2
/proc/490/fd:
total 0
lr-x------ 1 root root 64 Nov 3 2016 0 -> /tmp/fifo
root@bela:~# ps aux -q 414
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
root 414 0.0 0.2 1516 1120 ? S 14:01 0:00 /bin/sh -c sync& cd /root/Bela/projects/CommunityEchoTesting && /root/Bela/projects/CommunityEchoTesting/CommunityEchoTesting -p512 -C4 -B16 -N1 -G0 -M0 -H0,-6 -H1,-6 -H2,-6 -H3,-6 -H4,-6 -H5,-6 -H6,-6 -H7,-6 -I0,0 -I1
root 17 0.0 0.0 0 0 ? SN 14:01 0:00 [ksmd]
root@bela:~# ps aux -q 418
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
root 418 6.6 5.5 31848 27776 ? SLl 14:01 0:34 /root/Bela/projects/CommunityEchoTesting/CommunityEchoTesting -p512 -C4 -B16 -N1 -G0 -M0 -H0,-6 -H1,-6 -H2,-6 -H3,-6 -H4,-6 -H5,-6 -H6,-6 -H7,-6 -I0,0 -I1,0 -I2,10 -I3,10 -I4,10 -I5,10 -I6,10 -I7,10 -X0 -Z0,1,2,3
root 17 0.0 0.0 0 0 ? SN 14:01 0:00 [ksmd]
root@bela:~# ps aux -q 490
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
root 490 7.9 0.2 1428 1000 ? Ss 14:01 0:43 /bin/sh /root/Bela/projects/CommunityEchoTesting/fifo.sh
root 17 0.0 0.0 0 0 ? SN 14:01 0:00 [ksmd]
I confirm this happens when autorun is enabled