It seems newlines in stack traces have changed to contain only a line feed, not a carriage return. This makes emacs (correctly) consider the session logs to have inconsistent line endings. This seems to be a rather recent change.
There was a recent change that added stack traces to the session logs. However since they were not there before I'm a little confused about what you are saying. Would the following be a reasonable description?
Previous - session logs had consistent line endings and no stack traces.
Current - session logs have inconsistent line endings if, and only, if the log contains a stack trace.
s.append( "\n\u00A0\u00A0at " );
sb.append( KoLConstants.LINE_BREAK );
public static final String LINE_BREAK = System.getProperty( "line.separator" );