A friend helped me with this, and he realized that setting a border or background on the checkbox would make it look like this for some odd reason.
NGLN is correct, and I will agree to his answer. To do this, I had to change my CSS to the following:
textarea, select, input[type="email"], input[type="number"], input[type="password"], input[type="search"], input[type="tel"], input[type="text"]{ font-family:'ColaborateRegular'; background-color:#efefeb; border:1px solid; border-color:#89969f #89969f #cbcbc8 #89969f; outline: 0; padding:3px; width: 100%; margin-bottom:10px; -webkit-box-shadow:inset 0 1px 2px #b8b7b3; -moz-box-shadow:inset 0 1px 2px #b8b7b3; box-shadow:inset 0 1px 2px #b8b7b3; -webkit-box-sizing: border-box; -moz-box-sizing: border-box; box-sizing: border-box; -webkit-border-radius:4px; -moz-border-radius:4px; border-radius:4px; -webkit-appearance: none; -webkit-transition:background-color 0.4s, border-color 0.4s; -moz-transition:background-color 0.4s, border-color 0.4s; -ms-transition:background-color 0.4s, border-color 0.4s; -o-transition:background-color 0.4s, border-color 0.4s; transition:background-color 0.4s, border-color 0.4s; } input[type="radio"], input[type="checkbox"]{ margin:0 2px 0 0; } textarea:hover, select:hover, input[type="email"]:hover, input[type="number"]:hover, input[type="password"]:hover, input[type="search"]:hover, input[type="tel"]:hover, input[type="text"]:hover{ -webkit-box-shadow:inset 0 1px 2px #b8b7b3, 0 0 5px #7899b5; -moz-box-shadow:inset 0 1px 2px #b8b7b3, 0 0 5px #7899b5; box-shadow:inset 0 1px 2px #b8b7b3, 0 0 5px #7899b5; } textarea:active, textarea:focus, textarea:active:hover, textarea:focus:hover, select:active, select:focus, select:active:hover, select:focus:hover, input[type="email"]:active, input[type="email"]:focus, input[type="email"]:active:hover, input[type="email"]:focus:hover, input[type="number"]:active, input[type="number"]:focus, input[type="number"]:active:hover, input[type="number"]:focus:hover, input[type="password"]:active, input[type="password"]:focus, input[type="password"]:active:hover, input[type="password"]:focus:hover, input[type="search"]:active, input[type="search"]:focus, input[type="search"]:active:hover, input[type="search"]:focus:hover, input[type="tel"]:active, input[type="tel"]:focus, input[type="tel"]:active:hover, input[type="tel"]:focus:hover, input[type="text"]:active, input[type="text"]:focus, input[type="text"]:active:hover, input[type="text"]:focus:hover{ background-color:#f9f9f5; border-color:#658cae; -webkit-box-shadow:inset 0 1px 2px #b8b7b3, 0 0 8px #7899b5; -moz-box-shadow:inset 0 1px 2px #b8b7b3, 0 0 8px #7899b5; box-shadow:inset 0 1px 2px #b8b7b3, 0 0 8px #7899b5; z-index:1; }