I've received messages in eBay that do not show up in my account messages
Generally that indicates a message that has been removed by eBay, often for a policy violation such as sending contact information prior to a transaction payment.
There's a bug when searching seller stores, or maybe it's only noticeable when searching specific stores that this bug will show itself, since you're searching a smaller pool of items where you can confirm an item is there, but doesn't show up when searched for.
Can you provide an example of the search you are doing and the item that is not appearing in the search? There may be a reason the item is not seen, such as an item that is listed in the wrong category. eBay may steer a search into a particular category based on the search keywords, and if the listing is not in that category, it will not appear in that search.
If you think a search is not working right, there should be a feedback icon in the lower right corner of the search results if you are using a desktop browser. You can use that to contact eBay developers about search issues.
Other eBay pages may have a "Tell us what you think" link in the upper right corner to let page developers know about issues with a page feature.
