The -i flag specifies the private key (.pem file) to use. If you don't specify that flag (as in your first command) it will use your default ssh key (usually under ~/.ssh/).
So in your first command, you are actually asking scp to upload the .pem file itself using your default ssh key. I don't think that is what you want.
Try instead with:
scp -r -i /Applications/XAMPP/htdocs/keypairfile.pem uploads/* ec2-user@publicdns:/var/www/html/uploads