What is the best way to make .ISO files based on a file folder structure from C#? Is there an open source library other than DiscUtils? Running into issues
You could try Primo Burner: http://www.primoburner.com/Downloads.aspx
Here are some more to try
Windows actually comes with a native API for creating ISOs and much more: the Image Mastering API. Once you grab the IMAPI2 Interop assembly from the Windows SDK or (probably easier) from this CodeProject article about IMAPI2, creating an ISO is only a few lines of code.
Unfortunately, you also need a few paragraphs to properly clean up the COM nonsense involved, but the end result is still pretty manageable:
MsftFileSystemImage iso = new MsftFileSystemImage();
iso.ChooseImageDefaultsForMediaType(IMAPI_MEDIA_PHYSICAL_TYPE.IMAPI_MEDIA_TYPE_DISK);
iso.FileSystemsToCreate = FsiFileSystems.FsiFileSystemISO9660 | FsiFileSystems.FsiFileSystemJoliet;
iso.Root.AddTree(@"c:\path\goes\here\", false);
dynamic resultImage = iso.CreateResultImage();
dynamic imageStream = resultImage.ImageStream;
IStream newStream = null;
if (imageStream != null)
{
    STATSTG stat = null;
    imageStream.Stat(stat, 0x1);
    int res = SHCreateStreamOnFile(@"c:\path\to\your.iso", 0x1001, newStream);
    if (res == 0 && newStream != null)
    {
        IntPtr inBytes = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(long)));
        IntPtr outBytes = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(long)));
        try
        {
            imageStream.CopyTo(newStream, stat.cbSize, inBytes, outBytes);
        }
        finally
        {
            Marshal.FinalReleaseComObject(imageStream);
            newStream.Commit(0);
            Marshal.FinalReleaseComObject(newStream);
            Marshal.FreeHGlobal(inBytes);
            Marshal.FreeHGlobal(outBytes);
            Marshal.FinalReleaseComObject(resultImage);
            Marshal.FinalReleaseComObject(iso);
        }
    }
    else
    {
        Marshal.FinalReleaseComObject(imageStream);
        Marshal.FinalReleaseComObject(resultImage);
        Marshal.FinalReleaseComObject(iso);
        //TODO: Throw exception or do whatever to signal failure here
    }
}    
else
{
    Marshal.FinalReleaseComObject(resultImage);
    Marshal.FinalReleaseComObject(iso);
    //TODO: Throw exception or do whatever to signal failure here
}
Details for the only bit of Win32/COM API glue used can be found on pinvoke.net: SHCreateStreamOnFile. IStream and STATSTG are in System.Runtime.InteropServices.ComTypes..