Don't see what could be the problem. Here is the code I always use to create media. Always seems to work:

public Media InsertMedia(int parentId, string fileName, MediaType mediaType, User adminUser, byte[] bytes, bool isImage)
{
    Media media = Media.MakeNew(fileName, mediaType, adminUser, parentId);

    string sql = string.Format(@"
                select cpd.id as id from cmsPropertyData cpd
                    inner join cmsPropertyType cpt on cpd.propertytypeid = cpt.Id
                    inner join cmsDataType cdt on cpt.dataTypeId = cdt.nodeId
                where cpd.contentNodeId = {0}
                and cdt.controlId = '{1}'", media.Id, uploadField.Id);

    int propertyId = SqlHelper.ExecuteScalar<int>(sql);

    FileInfo file = new FileInfo(IOHelper.MapPath(SystemDirectories.Media + "/" + propertyId + "/" + fileName));

    if (!file.Directory.Exists)
    {
        //If the directory doesn't exist then create it.
        file.Directory.Create();
    }

    //Write the file to the media folder.
    File.WriteAllBytes(file.FullName, bytes);

    string umbracoFile = SystemDirectories.Media + "/" + propertyId.ToString() + "/" + fileName;
    if (umbracoFile.StartsWith("~"))
    {
        umbracoFile = umbracoFile.TrimStart(new char[] { '~' });
    }

    if (media.getProperty("umbracoFile") != null)
    {
        media.getProperty("umbracoFile").Value = umbracoFile;
    }

    if (media.getProperty("umbracoExtension") != null)
    {
        media.getProperty("umbracoExtension").Value = Path.GetExtension(file.Name).Replace(".", string.Empty);
    }

    if (media.getProperty("umbracoBytes") != null)
    {
        media.getProperty("umbracoBytes").Value = bytes.Length;
    }

    if (isImage)
    {
        System.Drawing.Image image = System.Drawing.Image.FromFile(file.FullName);

        if (media.getProperty("umbracoWidth") != null)
        {
            media.getProperty("umbracoWidth").Value = image.Width.ToString();
        }

        if (media.getProperty("umbracoHeight") != null)
        {
            media.getProperty("umbracoHeight").Value = image.Height.ToString();
        }

        //Create a thumbnail from the image.
        string fileNameThumb = Path.Combine(file.Directory.FullName, file.Name.Replace(Path.GetExtension(file.Name), "_thumb.jpg"));
        GenerateThumbnail(image, 100, image.Width, image.Height, fileNameThumb);

        //Clean the image.
        image.Dispose();
    }

    //Save the media file to update the xml to make sure some event's get called.
    media.Save();
    media.XmlGenerate(new XmlDocument());

    return media;
}

Jeroen