I have a Canon T3I that I received for Christmas. With the card in the camera, it shows I have over 400 pictures and I can view them on the camera screen. However, when I try to download them on my laptop it only recognizes 31 pictures. Same thing happened at WalMart in their card reader yesterday when I took it in there.
Did you shoot some pics in RAW by any chance? If so they may not be recognized.
Check and see if you have any *.CR2 (I believe that this is the extension for Canon RAW files) files on your memory card folder.
Rather than using the photo transfer utility that came on your laptop, try using Canon's EOS Utility that came on the software CD with your camera. Once installed, you can download free updates from Canon's T3i support page.
Files that are saved in raw format with an extension of .cr2 may not be recognized as photos by the generic import utility it sounds like you are using. EOS Utility or many other more robust photo applications such as Adobe Lightroom will also recognize and import the raw files along with the JPEGs.
You can check if the image files are present on the card by going to: My Computer, Your Card Name, DCIM
You should now be able to see one or more folders. All the photos you have taken should be stored in these folders. From here you can select all the images and drag and drop them into your computer.
As said above some of your images may be in RAW format (.CR2) instead of JPEG (.jpg). You can open RAW images using programs such as Digital Photo Professional (DPP), which comes with your camera. If you don't have DPP you can download it for free from Canon's website. http://www.canon.co.uk/support/consumer_products/product_ranges/cameras/eos/ Just select your camera from the list and you should be good to go!