I'm not saying it's impossible that something happened between my commit last night and today that I haven't tested to find this problem BUT you might try two immediate reactive approaches:
1) Delete the cache
2) Hit the ignore button when that popup comes up and see if it causes any problems.
In the meantime I'm searching for the reference you gave... the message didn't happen to include the file it was looking at did it?
I did delete cache and select ignore - the game just freezes.
When I try to attach a minidump file - I get an invalid file message.
The last few lines of the xml.log were:
[17863.828] SetDiplomacyInfo (/Civ4DiplomacyInfos/DiplomacyInfos/DiplomacyInfo)
[17863.828] LoadCivXml: Read Mods\Caveman2Cosmos\Assets\modules\Custom Leaderheads\Wu\Wu_CIV4DiplomacyInfos.xml
[17863.828] Load XML file Assets\modules\Custom Leaderheads\Wu\Wu_CIV4DiplomacyInfos.xml SUCCEEDED
[17863.828] SetDiplomacyInfo (/Civ4DiplomacyInfos/DiplomacyInfos/DiplomacyInfo)
[17863.828] LoadCivXml: Read Mods\Caveman2Cosmos\Assets\modules\Custom_Civilizations\Neanderthal\Neanderthal_CIV4DiplomacyInfos.xml
[17863.828] Load XML file Assets\modules\Custom_Civilizations\Neanderthal\Neanderthal_CIV4DiplomacyInfos.xml SUCCEEDED
[17863.828] SetDiplomacyInfo (/Civ4DiplomacyInfos/DiplomacyInfos/DiplomacyInfo)
[17863.828] LoadCivXml: Read ..\Assets\xml\Misc/CIV4QuestInfos.xml
[17863.828] Load XML file Assets\xml\Misc/CIV4QuestInfos.xml SUCCEEDED
[17863.828] SetGlobalClassInfo (/Civ4QuestInfos/QuestInfo)
[17864.172] LoadCivXml: Read ..\Assets\xml\Misc/CIV4TutorialInfos.xml
[17864.172] Load XML file Assets\xml\Misc/CIV4TutorialInfos.xml SUCCEEDED
[17864.172] SetGlobalClassInfo (/Civ4TutorialInfos/TutorialInfo)
[17864.516] LoadCivXml: Read Mods\Caveman2Cosmos\Assets\xml\GameInfo\CIV4EspionageMissionInfo.xml
[17864.531] Load XML file Assets\xml\GameInfo\CIV4EspionageMissionInfo.xml SUCCEEDED
[17864.531] SetGlobalClassInfo (/Civ4EspionageMissionInfo/EspionageMissionInfos/EspionageMissionInfo)
Not sure if that helps or not.
In the meantime I'm searching for the reference you gave... the message didn't happen to include the file it was looking at did it?
The file was: civ4Espionagemissioninfo.xml
Sorry that I missed that in my first post. But it was a long error message.
EDIT: Downloaded SVN again (now revision 7585) I can start a new game. Will try loading existing games later. It is to late at night now.
Maybe the previous download had a glitch in it.