I'm not sure (although I guess) I'm talking to the same person through facebook, so I'll c&p here what I've written there, so we would have a public copy of the thing
I had an odd issue with it one time, that after start it didn't want to work, see this:https://github.com/atarijookie/ce-atari/issues/99
So, run the test, see if it fails like before. Then connect to it using ssh, stop the linux app by running /ce/ce_stop.sh
...and then start the ce app again by running: /ce/ce_start.sh
then see if the test results are better or still bad.
Also: please check using 'top' or something similar if your system load is not high (using too much cpu %).
And it would be also nice to see if your linux boot is finished at that time - if you have a TV with HDMI around, connect it to HDMI of Raspberry Pi and see if the booting process finished, or still does something (like waiting for network or something).