Saving it as either a jpg or a pdf should not affect the quality. There may be other settings involved that do so. jpg is the format most often used for pictures that are going to be seen online. There are compression setting involved with a jpg file, so make sure you use as little compression as possible - that affects quality.

That document you attached shows that the scanner software is set to scan grayscale, not color. Change that, and your colors should reappear fine!