There are a number of issues with using the file picker in your own custom controls - in our experience we have found that its NOT a module that you should try to drop directly onto a .ascx file as a control.
Part of the reason for this - is that the control actual instantiates other controls inside itself BEFORE you are able to set some of the properties yourself,
Drop a placeholder control on you ascx page - thisPlaceHolder:
var userControl = Page.LoadControl("~/controls/filepickeruploader.ascx");
DotNetNuke.Web.UI.WebControls.DnnFilePickerUploader _fileControl = userControl as DotNetNuke.Web.UI.WebControls.DnnFilePickerUploader;
if (_fileControl != null)
{
_fileControl.ID = thisTarget;
// _fileControl.FileFilter = "jpg,jpeg,gif,png";
_fileControl.FileFilter = thisFileFilter;
_fileControl.UsePersonalFolder = true;
_fileControl.User = thisUser;
if (!Page.IsPostBack)
{
_fileControl.FilePath = filePath;
_fileControl.FileID = thisValue;
}
//Add table to Control
thisPlaceHolder.Controls.Add(_fileControl);
}