Yes, autosaves during autoplay have been disabled for speed reasons. Set the value of NO_AUTOSAVE_DURING_AUTOPLAY in GlobalDefinesAlt.xml to 0 to enable it again.
I don't think DoC can affect how many autosave files are stored, maybe it's somewhere in your settings?
Well not exactly but they are connected

The setting for amount of saves and interval between saves would be in the 'CivilizationIV.ini' in the 'Beyond the Sword' folder where the screenshots and saves folders are too.
I've watched the autosave folder during autoplay/and while skipping turns a bit while 'playing' different civs.
It has to do with either having autosave during autoplay enabled or starting on the first turn.
e.g. 600 AD/3000 BC (only 600 AD start tested, Japan/Byzantium/China)
If autosave during autoplay is enabled (via GlobalDefinesAlt.xml) the game first creates a save file like this one.
AutoSave_Initial_AD-0600 Turn 278.CivBeyondSwordSave
If that file is created all save files in the folder get deleted.
If you start a 'real' 600 AD start like with Japan, China, Byzantium that file is also created. All autosave files get deleted.
And the new autosave sequence begins.
If you start (and play a few turns: 20+ ) a game with lets say:
1st Japan (600 AD, all autosaves deleted.. 'Initial' autosave created)
2nd Arabia (620 AD, no delete)
3rd England (8xx AD, no delete)
4th Italy (11xx AD, no delete)
You end up with possibly around 12-16+ autosaves in that folder.
The more 'late' civs you play the more possible files get created.
No '
AutoSave_Initial_AD-0600 Turn 278.CivBeyondSwordSave' to clear the folder first since it is part of autosave during autoplay.
The max of 5 saves only applies if it's in sequence, based on turn/year?
e.g. 1900, 1904, 1908, 1912, 1916
Once it's 1920 the 1900 autosave gets deleted.
Now if you load a different game say date 1940, different civ too..
Autosave should start new from 1940 or 1944(4 turns)
The 1900, 1904 etc. autosaves should remain untouched.
And this could continue until the game clears out the folder(have seen up to around 30 saves in the folder due to reloading/continuing a game).
At least that save file is the only connection I have between whether or not the folder gets emptied or not on starting a new game.
I hope this is somewhat comprehensible, I'm having a hard time trying to explain it.. not even sure if it would work out better if I tried explaining it in german
My 'problem' might occur if I start a game with Prussia and then start one with say the Netherlands. Once I hit around the year 1700 when the Prussian autosave becomes relevant again I might have a freeze.
That is when the 1704 Dutch autosave tries to overwrite the 1704 Prussian autosave.
Autosaves don't contain civ specific info, just turn and year/era and I'm assuming that that's where my 'problem' is(double file/ file already exists error or something).
But the workaround for me is to simply enable autosave during autoplay
