I am a director at Majestic. (Nothing like personal service eh?
The Mathematics is the same - but the starting points are different. Citation Flow takes a logarithmic count of all of the links to any URL as a starting point, then iteratively FLOWS the strength of these scores through many links - so that a URL with a lot of inbound links can influence the score of a URL many links away. TRUST FLOW starts with a large (100s of thousands) of websites that we KNOW are looked at by humans. We assign these as our trusted set and then again flow this influence through links. In a purely random world, it would not matter where these calculations start - they would eventually (given enough links) mathematically come to rest at the same number - however - links are not natural and they are built up in different ways, so these metrics tend to be a little different to each other. Citation Flow correlates better with Page Rank (although the maths is different) but in my opinion, Trust Flow is a better metric of the quality of a URL. Not sure if Sitepoint will let me embed a link on my first ever post on Sitepoint - but I did a training video on it at http://blog.majesticseo.com/training/link-metrics-for-the-future-welcome-to-flow-metrics-video/.
Dixon Jones (For Majestic SEO).