Tomy,
I believe it is one of your plugins which is causing this issue.
You have 61 plugins installed with 45 active– that is a lot of plugins and I would advise that you consolidate to only those which you truly need for your site, as there are bound to be other conflicts with that many plugins- as well as a very heavy load on your site.
To repair the misaligned text and the black background, please try this in your theme/child theme styles.css:
.wcv-form p.tip {
text-align: left;
background-color: #fff;
}
In am still working with the filters to properly remove the shipping options without leaving the wrapper/div