@jenkutler I am not sure at all.
Maybe just the path to the Pd folder then.....
Or just the path to /extra........?
and not the path all the way to cyclone.
Normally the path to the "extra" folder where the libs are stored is automatically set. But maybe not with -nogui........?
It is set with the switch -stdpath
There is more info here....... http://write.flossmanuals.net/pure-data/advanced-configuration/
You could try to set it, and that might be all that is necessary?
pd -nogui -stdpath -lib cyclone /home/pi/Desktop/theOther/theOtherV5.pd &
But the real question is why the -nogui switch is breaking Pd.
Grubbing around for other problems with -nogui finds that patches are normally loaded after the Gui has built (there is a delay so that the Gui can complete).
But with -nogui the patch is loaded before Pd has connected all of its parts. audio, midi etc. and maybe its libraries?
So maybe ignore all of the above.
If there is a way to delay the opening of "theOtherV5.pd" in the script then that might solve the problem.
Also Pd "knows where it is" from its command line...... and maybe you are not invoking the normal shortcut with your script.
root/path_to_pd/pd -nogui /home/pi/Desktop/theOther/theOtherV5.pd &
All straws clutched I think.