ok, Answering my own question here! I checked the advanced tab in the settings and the 'Don't compress saves' wasn't ticked. I ticked this and tried again. Still wouldn't load the save.
So, I loaded up the 5.003 save and immediately re-saved this file. I then evaluated my latest 5.004 save that won't open with the fresh 5.003 converted save and found that the 5.004 save that doesn't open has this at the top; COMP 5.004
The fresh save doesn't! So I deleted that line and re-saved the file manually (I used EmEditor, as notepad won't line break correctly) and tried loading the save.....
It works!
So it looks like the game is saving them oddly if that 'Don't compress saves' isn't ticked. It looked like they were uncompressed, but had a compressed header (I believe that's what COMP means)
Old 5.003 save looked a little like this;
COMP 5.003
EGcRAB+LCABhNYFNAP <SNIP>
5.004 save that won't load looked like this;
COMP 5.004
5004|1
19|11314
46|1,1,60,2,,0,0,0,1,1,1,1,1,1,1,1,0,0,1,0,-1,False,,,,,1,2,1,0,1,1,
and the 5.004 file that does load after being re-saved with the 'Don't compress saves' box ticked looks like this;
5004|1
19|11314
46|1,1,60,2,,0,0,0,1,1,1,1,1,1,1,1,0,0,1,0,-1,False,,,,,1,2,1,0,1,1,