The problem stopped. Only changes I had been making were in Centers of Trade, which were simply things to empower lesser states, eg: Reinstating Corfu
However, now I have a different problem that is only occurring to my Bavaria game. When I click on it to load it at the game start, the game freezes. All other save files worked normally.
I have my suspicions (bless you, Firefox Spellcheck!) it is because I trawled through the country descriptions finding the problematic ones before starting the game (I draw this suspicion from the little box displaying all of the country names when you load the file).
Also, as it is better here than in Little guy, the countries and their missing DESC files:
Altmark
Anhalt
Franconia
Galicia
Gotland
Hannover
Il-Khanate
Istria (I don't think this country actually exists at gamestart. . . but it is selectable)
Kiev
Krete
Koln (not actually missing, is only a one liner about it being a cool city)
Languedoc
Leon
Lu Chuan
Milan
Moldavia (doesn't say it is missing, but is entirely blank)
Nazhao
Navarra (see Moldavia)
Porto
Romagna (also has a shield/flag error, it looks like Smolensk's is there)
Silesia
Smolensk
Styria
Toluid Khanate
Tuscany (see Moldavia)
Tyrol
York
Also found a few questionable things:
In the Lollardy Dominates events, it seems Kent and Wessex are mixed up (as in, the event talking about Wessex affects Kent).
One of the events concerning the Lollard Deren has 'wyclif' instead of 'Wyclif'
The description of Maya: Towards the end it mentions west when it should be east (I'm not 100% certain about this one, it may be I am wrong about the description or have the directions backwards)