Using "Restrict by app" in change query causes issues with Search Results

Hello!
I am hoping some experienced SP admin can help me out. I am having issues with the relevance ranking for my search results web part.
I created a Wiki (OOTB) within a site collection and on the home page of the Wiki I was looking to apply a Search Box and Search Results web part for easy searching. I wanted to ensure the search results were restricted to the scope of the pages within the
wiki. I did the following after adding the 2 web parts:
Entered edit mode for the page
Started to edit the Search Results web part
Under Properties for Search Results clicked on "Change Query"
Navigated to BASICS and clicked "Switch to Quick Mode"
For Select Query, picked "Wiki (System)" option
For Restrict by app, picked "Specify a URL" and input the wiki URL "http://webapp.com/sites/sitecollection/wiki"
Click OK
The web part has 6 automatic results when I hit the page. These are the only 6 pages in my wiki. When I search a word or title of a page, they are not ranked in order or relevance. The ordering is static to what was being shown before the search, but the
keywords I'm searching are bold. With out the taking the steps above, I can easily search these pages and have them ranked appropriately so I'm not too sure what I'm doing wrong. 
Other Details
The pages have been crawled and can be searched from anywhere else in SP.
I am only a site collection admin for this specific site collection.
I other than the steps above, I have not made any changes or customization to the search web parts; they are both out of the box SP.
The SP Farm admin we unable to pin point what the root cause is either.

Hi Mikael,
Sorry for the wait, I was unable to post pictures, which i felt would better describe my issue.
Could you output the query template you are ending up with?
If you can tell me how to accomplish this, then I can provide it. Please keep in mind that I am only a site collection admin.
Also, is the ranking/sorting for your webpart set to ranking?
When looking at the web part settings, I didn't see an option to modify the ranking. Unfortunately, some sites in my intranet are down now so I can't even double check. Once it's back up, I will verify this as well.
And how do you know they are ranked incorrectly?
I wanted to display an image showing what I meant by this. As the wiki is down, I'll do my best with words. When I visit the wiki home page, I already have the search and search results web parts there. Without searching anything, the search results
web part displays 6 pages that are available in the wiki. When I search, I expect to see the most relevant result at the top. similar to the following: 
*Search result from another section of the intranet site.*
What I receive instead is the same list of wiki pages, in the same order. The most relevant result
is not moved to the top like in the image above, but I can see that the word "rush" is highlighted in bold. I hope this helps.
If you need more of a description, please let me know.
Thank you

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