The emulated EQ servers have to deal with the boxing issue more than any others because they emulate the older, simpler game which allows running many clients on one machine and slow gameplay allows for easy boxing.
The Al'Kabor Project went with a 3 box limit (against my pleas), and four years later most of the userbase wishes they had gone with limit of 2 instead.
What ended up happening is that raids are full of wizard and cleric throwaway 3rd characters that provide DPS and healing for the rotations while they 'main' the one character they like. (2nd box is usally an enchanter, or whatever helps them solo) Any DPS or healing checks on raid bosses are irrelevant when you can field armies of wizards and clerics that you alt-tab to and mash the nuke and heal button. The emotional attachment to these boxed characters is absent; they funnel loot to their primary character so these characters get BIS in everything as the guild has half as many real players or less; everybody feels pressured to make boxed wizards and clerics instead of other classes; 15+ clerics on a raid trivializes any sort of endurance or recuitment challenges; boxed melee characters end up standing next to raid bosses without auto attack on. (seen this many times) Powerleveling becomes insane when you have so many enchanters and wizards around to PBAoE and it only takes two people to form AoE groups. etc
Furthermore the grouping game ended up with most of the server soloing on their 3 boxes instead of seeking groups, and solo players feel pressured to box because they cannot find groups and they get out-competed by boxers. Raiders, out of greed, are tempted to 3 box instead of 2 or 1 box so they end up losing or just raid slow because performance-per-character suffers significantly when boxing. Not to mention that non-instanced games have the issue of limited spawns and 3 boxes allows a 10 person guild to kill the NToV dragons, so 30 people means three guilds instead of one, which results in more interguild drama. The 1 box limit was the smartest thing Project 1999 did.
People have to be forced to group or they won't do it. They'll bitch and whine about it but after they do it, they enjoy it more than soloing. EQ is really a 'users don't know what's best for them' kind of game.