I'm having the same error, with the new verion just downloaded, the references are ok.... but 5 pages gives that error:
Error 1 Unknown server tag 'CE:UploadSingleFile'. C:\inetpub\wwwroot\Cartocor\CuteSoft_Client\CuteEditor\Dialogs\Gecko_InsertMedia.aspx 217
Error 2 Unknown server tag 'CE:UploadSingleFile'. C:\inetpub\wwwroot\Cartocor\CuteSoft_Client\CuteEditor\Dialogs\Gecko_InsertImage.aspx 264
Error 3 Unknown server tag 'CE:UploadSingleFile'. C:\inetpub\wwwroot\Cartocor\CuteSoft_Client\CuteEditor\Dialogs\Gecko_InsertDocument.aspx 184
Error 4 Unknown server tag 'CE:UploadSingleFile'. C:\inetpub\wwwroot\Cartocor\CuteSoft_Client\CuteEditor\Dialogs\Gecko_InsertFlash.aspx 244
Error 5 Unknown server tag 'CE:UploadSingleFile'. C:\inetpub\wwwroot\Cartocor\CuteSoft_Client\CuteEditor\Dialogs\Gecko_InsertTemplate.aspx 141