The anti-cheating mechanisms were put in place by Lizthegrey in an attempt to end players abusing alts for higher stats.
Aside from being able to "track every single PoE in the game, from the very beginning", Liz has also said she has systems to detect "thrown" swordfights (and, presumably, other parlor games), which were a popular way of boosting one's standing and experience until the clampdown1. Prior to this, one could play against their own alt and have the alt dismiss the puzzle repeatedly until the standing and experience desired was achieved.
Unrated parlor games are not subject to the anti-cheating mechanisms.
1On April 3, 2006, Lizthegrey implemented a "cleaning" process on each ocean which reset many pirates' puzzle experience and standing to Novice/Able based on findings of the anti-cheating mechanisms, thereby removing those pirates from the Ultimate list.
Additional cheat detection was introduced for swordfighting in release 2006-04-06.
On July 15, 2006, Lizthegrey stated that she would no longer only reset the standing of cheating pirates; instead, she would ban them. At least 24 accounts were initially banned.