Problems Accounting for Multi-Way Pots
The problem that both Hold’em Manager and PokerTracker 3 have with accounting for multi-way pots has to do with unknown holecards. In order to make an accurate “EV” (results-oriented) calculation, the software must know the holecards of all players in the hand at the time Hero went all-in — even the holecards of the hands that were folded.

Of course, unless you are a superuser, this is impossible to know.

Let’s say it’s no-limit hold’em and three players put in $25 each before the flop. The starting stack sizes and hands are as follows:

Hero ($100) — A♠ A♦
Villain A ($400) — K♠ K♦
Villain B ($400) — 9♠ 9♦
Flop ($75): 3♠ 2♦ 2♥. Hero pushes all in for $75, and both Villain A and Villain B call.
Turn ($300): XX (any card). Villain A pushes all in for $225, and Villain B (?).

Here’s the problem: Let’s say Villain B only calls if the turn is the 9♥ or 9♣ — that is, if he can beat A-A — but folds if the turn is any other card. What happens is that 41 out of 43 times, for the purposes of the All-In EV calculation, Hero shows up as having 91.616 percent all-in equity against the K-K hand. However, two out of 43 times, Hero shows up as having 82.946 percent equity against both the K-K and 9-9 hand. This happens even though Hero was all in against both opponents at the time Hero went all in.

This is clearly incorrect.

EV if Turn is Non-9 (41 out of 43 cards)
Player All-In Equity Pot Size EV All-In EV
Hero 91.616% $300 $274.84 $174.84

EV if Turn is 9 (2 out of 43 cards)
Player All-In Equity Pot Size EV All-In EV
Hero 82.946% $300 $248.84 $148.84

Consequently, if poker-tracking software were to count this hand in its All-In EV calculation — as Hold’em Manager appears to do — the software will systematically overestimate Hero’s All-In EV. As a result, users as a group will tend to appear unlucky.

PokerTracker 3, on the other hand, does the opposite and does not account for this hand at all for the purposes of calculating All-In EV, and instead only makes the “EV” adjustment when all holecards of callers are known. Unfortunately, this method is not quite optimal either, as accounting for multi-way pots in which all cards are known without accounting for multi-way pots in which hands are folded should result in a smaller bias in the other direction (i.e., the user should theoretically appear slightly lucky rather than very unlucky), but a bias nonetheless.