This change is as far as I know kind of breaking the fix protocol definition of timestamps but that's another story.
There is a static class in QuickFixn called DateTimeConverter under QuickFix/Fields/Converters.
To get this to work correctly you would need to add format strings in lines in that class.
Add "yyyyMMdd-HH:mm:ss.fffffff" to DATE_TIME_FORMATS and "HH:mm:ss.fffffff" to TIME_ONLY_FORMATS so that it would look like this.
/// <summary>
/// Convert DateTime to/from String
/// </summary>
public static class DateTimeConverter
{
public const string DATE_TIME_FORMAT_WITH_MILLISECONDS = "{0:yyyyMMdd-HH:mm:ss.fff}";
public const string DATE_TIME_FORMAT_WITHOUT_MILLISECONDS = "{0:yyyyMMdd-HH:mm:ss}";
public const string DATE_ONLY_FORMAT = "{0:yyyyMMdd}";
public const string TIME_ONLY_FORMAT_WITH_MILLISECONDS = "{0:HH:mm:ss.fff}";
public const string TIME_ONLY_FORMAT_WITHOUT_MILLISECONDS = "{0:HH:mm:ss}";
public static string[] DATE_TIME_FORMATS = { "yyyyMMdd-HH:mm:ss.fffffff", "yyyyMMdd-HH:mm:ss.fff", "yyyyMMdd-HH:mm:ss" };
public static string[] DATE_ONLY_FORMATS = { "yyyyMMdd" };
public static string[] TIME_ONLY_FORMATS = { "HH:mm:ss.fffffff", "HH:mm:ss.fff", "HH:mm:ss" };
public static DateTimeStyles DATE_TIME_STYLES = DateTimeStyles.AssumeUniversal | DateTimeStyles.AdjustToUniversal;
public static CultureInfo DATE_TIME_CULTURE_INFO = CultureInfo.InvariantCulture;