Primary Nav & Secondary Nav not aligned

The primary nav and secondary nav are not aligned. Even when the secondary one inherits the primary, it doesn't seem to inherit the vertical element spacing. Maybe it is caused by a plugin that i use which fixes the navigation bar on scroll and transitions to a white background, this is the following code:

.Header { position: fixed!important; z-index: 1000; width: 100%; -webkit-transition: all .2s ease; -o-transition: all .2s ease; transition: all .2s ease;}

.Header-inner { padding-top: 50px; -webkit-transition: all .2s ease; -o-transition: all .2s ease; transition: all .2s ease;}

.Header.scrollNav { background: #fff!important; padding-bottom: 10px;

.Header-inner { padding-top: 10px!important; }

.Header-branding { color: #000; }

.Header-nav a { color: #000!important;

&:hover {
 color: rgba(0,0,0,.6)!important;
}

}}

@media screen and (min-width: 640px) { .Index section:first-child, .Main--page, .Intro, .Main { padding-top: 81px; }

.Intro + .Main { padding-top: 0px; }}

You can look at the screenshot i uploaded. Furthermore I want to keep the plugin if possible while the secondary navigation (or primary) aligns with the rest of the navigation bar.