First things first:
Please note that the test on https://www.magereport.com is not capable of highly conclusively checking customized shops and even has troubles of checking particular patches if certain other patches are installed. Therefore you must understand that MageReport.com - even though I highly appreciate there effort and still would like to recommend using this tool as a quick, first check - is NO ultimate, omnipotent testing tool and only can work within certainly given limitations.
As an example:
In your case magereport.com is not able to figure out what version of Magento you're using. This check is based on its own Version Identification using hashes of some static files (see gwillem/magento-version-identification on GitHub).
Edit: For those of you who want to run the version check by yourself you may be interested in the equivalent steverobbins/magento-version-identification-php on GitHub. Installation and usage is described in the help page (though I wont post it here since this in my opinion is not relevant to the actual question).
Basically, the disclaimer (FAQs on MageReport.com) already tells a lot about the process:
It's our first priority to make our security checks accurate. While we
thoroughly test and constantly tweak our security checks, we cannot
guarantee that the results are always 100% accurate. Every Magento
store is different, and in some scenarios, the configuration of your
store or server may lead to false positives or negatives. Therefore,
we advise you to use MageReport as a guide. If you are unsure about
the validity of a check, please consult your developer or find one on
the support page.
Edit: What you could do, in case this is applicable for you is to specify the actual backend URL (in case your backend is not reachable at "/admin"). However, I strongly believe that your main problem is the fact that there is some mismatch in your file hashes - in worst case due to core file changes! This said MageReport.com might fail since it can not check for applied differences since it doesn't know what to look for in your setup (because it would need to check for EVERY Magento version available...). You can determine if this is the case for example by using the Magento Security Council's Integrity check available on GitHub.
However, in order to address your situation a bit more clearly as MageReport.com (in general) is able to determine the state of the mentioned patches:
I would assume you checked on this but first of all you must make sure that the particular patch is actually applied completely. Especially if a patch was not applied via SSH but manually by modifying files based on diffs or similar approaches.
"Completely" already brings me to the next topic. When patching a shop you will patch exclusively the files Magento ships with. That being said any custom skins/themes (i.e. templates residing in folders such as
app/design/frontend/my-shop/my-style) will NOT BE PATCHED! You will ALWAYS have to apply changes on them manually by checking what a given patch is actually changing and integrate these changes into your theme.
The exactly same thing applies on any custom module - self-written or purchased. If you, as an example, are overwriting a particular function that got patched by a "SUPEE" you must make sure that this change is reflected in your custom code as well.
Alternatives to patching you shop the "common way":
Security patcher from 'Magento security council: https://github.com/magesec/magesecuritypatcher
Mage Security Patcher is a more effective alternative to the standard
magento patches. Patching Magento is prone to failure because you are
applying patches over patches, and sometimes even multiple versions of
patches. Figuring out what patches you need and what versions is also
painful and error prone.
Instead, this patcher updates the entire Magento installation to a
fully patched state - automatically. It works 100% of the time,
because instead of applying individual patches and building up patched
files, it patches your Magento installation directly to the final
state of having all patches applied. It also adds in form keys to
custom templates that would not be included in the standard patch
Rather than patching a shop it is always an option to run a complete update.
Both alternatives however still require you to make sure that any customization is in tune with the given Magento version / patch state.