The difference is naturally occurring links from regular non paid diversified sites vs paid links from directory type sites that Google has already flagged as being bad neighborhoods used for SEO, and these sites are most likely linking to a lot of penalized sites as well which makes you guilty by association.
So it has more to do with the places you are linked on than it does overusing your brand name in the anchor text, plus naturally occurring links will have their own keyword mix and match diversity.
brandname
visit brandname
visit brandname.com
go to brandname
some will be do follow, some will be no follow, some might be image links