Hi There,
Just to explain what is happening, making certain element, in this case topbar fixed means it is floating. It will take space on top of every other content. That means the logo and the menu will go behind the topbar. Now, it is not happening on large screen size because you have set NAVBAR TOP LOGO ALIGNMENT (PX) to be 60px. It moves the logo down.
Then those margin top 60px from settings was overridden by your custom CSS, from 60px values, it is now 20px. This then move the logo up again behind the fixed topbar:

Now to solve this issue, please remove that CSS that define margin top inside 1300 media query, and then add this instead:
@media (min-width: 980px) and (max-width: 1199px) {
body.x-navbar-fixed-top-active .x-navbar-wrap {
margin-top: 45px; /*45px is the height you specified for the topbar*/
}
.masthead-inline .x-btn-navbar {
display: inline-block;
float: right;
margin-top: 79px; /*Depending on the height of the logo, adjust this to center the mobile button vertically*/
}
}
@media (max-width: 978px){
.x-brand {
margin-top: 20px; /*On this 978px width is where we need to adjust margin*/
}
}
Then remove this custom CSS too:

Please be careful on adding CSS inside media query. Make sure that it is on specific size only. To test it, we can always use browser developer tools: https://developer.chrome.com/devtools
Hope this helps.