On Ubuntu linux version 12.04 using Pymol 1.4.1 installed via 'apt-get install pymol'. 64-bit AMD processor, 12 cores.
You can reproduce this bug by putting the following commands into a file called "bug_script" and then running 'pymol -c -p < bug_script'. On my machine, it almost never saves the 1M1J.obj file even though it always saves the 1M1J.pdb file.
When I run the set of commands within the standard pymol command window, they work fine. They work even if I paste them all at once.
When I run them using the -p and -c options and then paste them into the command line all at once, they often do not write the 1M1J.obj file, even though I get "Pymol: normal program termination". If I run all of them except the "quit" command, I do get the obj file all the time.
Looks like some sort of race condition.
This is a problem for me because I want to harness pymol inside a VR GUI program and use its excellent functionality to perform tasks that are needed.