I'm not sure which or how many of the pak files need to be executable, but when I had moved them back to the default location from a backup on my SD card (where their permission had been set to the FAT32 non executable default value) the game would not run.

The game was able to start again after I did a chmod -R 777 on the pak file's directory.

Maybe there was something else at work and this was just a coincidence, but after all the problems with WebOS game permissions, the execute flag is what I first though of.