Thanks for your prompt response Jake.
No to all your questions. I am truly baffled, because I didn't have this issue until very recently and I don't know how to solve it.
Any suggestions you can provide will be highly appreciated.
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I think I have found a solution, I however need to understand what’s going on better.
My solution: I checked the URL of my older layers on Portal for ArcGIS that are fine and noticed that they all were from the third URL. However, my newer layers that have been giving me problems were from the first and second URL. So, what I did was copy the affected layer urls from the third path and all is well again.
What I hope you could explain to me, is why I have these varying service URLs.
The 3rd URL is bypassing the web adaptor. You may want to check how you have the web adaptor's authentication set up. You can do this by going to IIS Manager (start > run > inetmgr) > Sites > Default Web Site > arcgisserver > Authentication. You will see something similar to below.