You haven't given many details, but I have a strong suspicion of what is wrong. Your camera is set to take pictures in RAW. It happens that for this model, RAW isn't available in the full-auto/scene modes, so in that case, it falls back to saving JPEG files.

There are two basic ways to resolve this. One would be to leave your camera as-is and use software which recognizes Canon's .CR2 RAW files. The other is to configure your camera to save JPEG files in the more-advanced modes as well. Look at page 64 of your manual, and change the setting to either one of the JPEG modes ("L", "M', "S"), or to "RAW + L", which saves both types of files. (This uses more space on the card, but gives you the most flexibility and is my personal preference.)

If you chose to use RAW, you'll need software which understands that. Canon offers free downloads on their web site for basic viewer and converter software for many operating systems. Many people prefer to invest in a more sophisticated program like Lightroom (which gets generally strong accolades from everyone). There are also various free software solutions, like RawTherapee.