I have recently converted all our EXPLODED caches into COMPACT caches and I think our missing.png and missing.jpg files no longer work for areas with missing data. I did re-add them into the correct folder according to the documentation.
Judging from the docs there is nothing that mentioned storage formats.
How To: Configure the cache folder to display a 'Data not available' tile for empty map cache areas or missing tiles
Does anyone have a missing.png or a missing.jpg file working when their cache storage format is COMPACT?