Sudden Misalignment of Masonry Layout

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Hi,
I'm a newbie to WP, so go easy on me please! I've been making a digital magazine and was NEARLY finished, until suddenly - out of my two rows of three images on the homepage - the sixth article/image decides to jump, after I modified the nav bar...! I'd include a picture but I can't, with the links rule.



I just want it in line with the others, and to be the last article on the line. I'm using the Sydney theme. Here's my additional CSS. Although, I've taken all the extra CSS out and it's still bugging.

Code:

#masthead.site-header {
  background-color: #18142c;
  height: 53px;
  padding: 9px;
}

.site-logo {
  width: 240px;
}

.single #content.page-wrap {
  background-color: #18142c;
  float: none;
  border-color: #18142c;
}

#mainnav ul li a:hover {
  color: #df60e3;
}

.overlay {
  height: 0px;
}

.single .page-wrap .content-wrapper {
  display: block;
  margin-top: -83px;
  text-align: center;
}

.col-md-9 {
  float: none;
  display: inline;
}

.panel-grid-cell .widget-title {
  top: -1200px;
  font-size: 50px;
  color: #ffffff;
  font-weight: 800;
  left: -250px;
  margin-top: 40px;
  text-transform: capitalize;
}

p {
  font-weight: 400;
}

.panel-row-style {
  font-size: 17px;
  margin-bottom: -190px;
  text-align: justify;
}

.hentry .title-post {
  text-align: center;
  margin-top: -306px;
  position: static;
}

.hentry .meta-post span {
  text-align: right;
}

.entry-date.published {
  text-align: right;
}

.entry-footer {
  text-align: center;
}

#commentform.comment-form {
  text-align: center;
}

#comment {
  text-align: center;
}

.sidebar-column.col-md-12 {
  margin-top: -590px;
  right: -470px;
}

.roll-button.button-slider {
  padding: 10px;
  right: 60px;
  bottom: 80px;
  background-color: #d64dd6;
}

.contain.animated.fadeInRightBig.text-slider {
  bottom: 100px;
}

.hentry .meta-post {
  margin-top: 270px;
}

#post-118.post-118.post.type-post.status-publish.format-standard.has-post-thumbnail.hentry.category-uncategorized {
  text-align: center;
}

#post-116.post-116.post.type-post.status-publish.format-standard.has-post-thumbnail.hentry.category-uncategorized {
  text-align: center;
}

#post-176.post-176.post.type-post.status-publish.format-standard.has-post-thumbnail.hentry.category-uncategorized {
  text-align: center;
}

#post-179.post-179.post.type-post.status-publish.format-standard.has-post-thumbnail.hentry.category-uncategorized {
  text-align: center;
}

#post-172.post-172.post.type-post.status-publish.format-standard.has-post-thumbnail.hentry.category-uncategorized {
  text-align: center;
}

#content.page-wrap {
  height: 3000px;
}

.so-widget-sow-image-default-642c5433d908 .sow-image-container .so-widget-image {
  overflow-x: visible;
  overflow: visible;
  overflow-y: visible;
}

.sidebar-column.col-md-3 {
  width: 02px;
  margin-top: -2100px;
  margin-left: -60px;
}

#sidebar-footer.footer-widgets.widget-area {
  height: 100px;
}

.widget-area .widget-title {
  color: #18152b;
  margin-top: -1080px;
  width: 160px;
  margin-left: 560px;
}

.roll-button:hover {
  background-color: #9345c8;
}

.textwidget {
  width: 1000px;
  text-align: center;
  position: absolute;
  color: #ffffff;
  font-size: 30px;
  margin-top: 150px;
  margin-left: 100px;
}

.posts-layout {
  line-height: 32px;
}

.single .textwidget {
  display: none;
}

.single .sidebar-column.col-md-3 {
  display: none;
}

.postid-176 .header-image {
  height: 500px;
}

.postid-176 .hentry .title-post {
  display: none;
}

.postid-176 #main.post-wrap {
  margin-top: -301px;
  line-height: 30px;
}

.postid-179 .header-image {
  height: 500px;
}

.postid-179 #main.post-wrap {
  margin-top: -320px;
  line-height: 30px;
}

.postid-179 .hentry .title-post {
  display: none;
}

#mainnav.mainnav {
  width: 1440px;
  margin-right: -1360px;
}

#menu-item-30.menu-item.menu-item-type-post_type.menu-item-object-page.menu-item-has-children.menu-item-30 {
  margin-right: 400px;
}

.entry-header {
  text-align: center;
}

.entry-post p {
  text-align: center;
}

.col-md-4.col-sm-8.col-xs-12 {
  margin-left: -200px;
  margin-right: -500px;
}

.li.icon-facebook a {
  font-size: 2px;
}

.postid-172 .header-image {
  height: 600px;
}

.postid-172 #main.post-wrap {
  margin-top: -310px;
  line-height: 30px;
}

.postid-172 .hentry .title-post {
  display: none;
}

.postid-118 .header-image {
  height: 600px;
}

.postid-118 #main.post-wrap {
  margin-top: -310px;
  line-height: 30px;
}

.postid-118 .hentry .title-post {
  display: none;
}

.postid-116 .header-image {
  height: 600px;
}

.postid-116 #main.post-wrap {
  margin-top: -310px;
  line-height: 30px;
}

.postid-116 .hentry .title-post {
  display: none;
}

.postid-116 #content.page-wrap {
  height: 3700px;
}

.postid-112 .header-image {
  height: 600px;
}

.postid-112 #main.post-wrap {
  margin-top: -310px;
  line-height: 30px;
}

.postid-112 .hentry .title-post {
  display: none;
}

.page .hentry .title-post {
  display: none;
}

.page .widget-area .widget-title {
  display: none;
}

.page .header-image {
  height: 600px;
}

.page #main.post-wrap {
  margin-top: -120px;
  line-height: 30px;
}

#menu-item-312.menu-item.menu-item-type-post_type.menu-item-object-page.menu-item-312 {
  padding-right: 350px;
}

#post-112.post-112.post.type-post.status-publish.format-standard.has-post-thumbnail.hentry.category-live.category-reviews {
  margin-left: -20px;
}

If it's not the additional CSS that's messing it up, however, does anyone know what it might be? I'm really struggling here. I was so close to getting it done and now can't find the source of the problem. Hopefully someone has some ideas, that would help me massively Thanks!