Psninja is badly outdated & does not do as good a job as psnpatch due to a missing core feature. Also it is completely unnecessary as you already use psnpatch.
Using the 3 tools together is utterly redundant & more likely to give you some conflicts or worse than help with anything. This is not an opinion, it's a fact.
You should choose between SEN Enabler & psnpatch and stick to it.
Regarding the ban risk factor, both tools do the same thing really so I doubt it will be less risky to play Fifa 2017 with SEN.
The biggest risk comes from the Fifa game servers & there's no way to tell what those servers may be checking on the console. Remember that if they really want to know if you are on CFW, they can, there isn't a single tool available that can stop them.
Try to minimise risks, use SEN or psnpatch & always follow the steps, spoof your ids with a spare set from a dead console, use a "blank" PSN account & avoid using mods or cheats when playing online.
As to SEN giving you trouble, are you using the plugin or the app?
Have you tried loading the plugin on its own without psnpatch & Psninja?
Have you checked the contents of your SEN configuration files to see if there was anything wrong there?
Edit: sorry kozzy I must have started to type just as you posted... [emoji6]