I've looked into it and could only half reproduce it but do you use Rich Markdown plugin?
Especially this option:
If so try to disabling it and see it works for you.
If you don't want to disable it or you don't have Rich Markdown
try this css:
.CodeMirror-line {
padding-left: 10px !important;
}
.CodeMirror pre.CodeMirror-line, .CodeMirror pre.CodeMirror-line-like {
padding-left: 10px !important;
}
Its a bit shot in the dark but for now its all i came up with.
Let's see if it fixes it.