Thanks so much EctoOne, that was some sharp eyes :D
I tried to simplify the structure previously by using variables to populate filenames but this ended up causing issues. Changing back to the file structure and hardcoding the names of each graphic seem to fix that. I thought I was done with messing in them sub-theme files and didn't think to check in there.
I was hoping to find that these problems where linked with the memory issues but alas, these problem with random missing images still prevails. Not to worry.