We already update our theme for compatible with latest version of WooCommerce and don’t get your issue. We also didn’t hear any issue like this from other customer.
About the issue with Header you should set them it Theme Options -> Header -> Header Elements.
More detail about Header and Logo please see in this topic:
In our theme have a notice that Page Options will override Theme Options. You can understand more about it follow this topic:https://harutheme.com/forums/topic/why-theme-options-doesnt-apply-changes/
Hope this help!