I have seen similar issues when looking at click throughs from Adwords banners.
What I have found is they are always often considerably disparate. They will likely never come close to matching for several reasons.
Firstly can you ask facebook do the click throughs they report account for viewable click throughs or all page click throughs? For example if an add is way below fold of a page.
Many online ads today are triggered by bots and crawlers so they are counted as a click through(by banner server) but then do not even allow your page to load completely or allow your analytics beacon to fire. Have a look as well to your page load speeds in extreme cases long page load speeds drop some of your potential conversion numbers. Also look at cookie duration of ad server, as often long cookie durations over inflate(in my opinion) traffic and click volumes of users who are actually of most relevant interest.
Another area today we see is actual browser setting of "DO NOT TRACK" being turned on. This can kill analytics cookie tracking and account for some users not being tracked as well.
In my experience your own site defined metrics should be your final KPI measure of success. So in your case ensure the KPI of a Complete Registration is setup correctly to fire, and ensure your ECID/ICIDs are well organized to allow for very granular tracking of users visits. When a real human user clicks that banner, then completes registration within a reasonable timeframe you will then have the most useful data to tell you what creatives were indeed the most successful.
I don't know what metrics you guys choose for analyzing facebook ads campaign but according to my knowledge if you are getting your objective on your facebook ads then here is some metrics that you should analyze that either they are running well or there is some changes required in it.