Yes it's how the rake is taken.
At Full tilt at 2/4 the rake is essentially taken in $1 pieces up to the $3 maxiumum at $60 (FWIW I'm pretty sure Stars is better here with a $70 pot needed for $3 rake and it needing to be 6 people playing not 5-6 but whatever)
At Ipoker it's a flat 5% rake. So the only time the rake structures are equal is if the pot is exactly $20, $40 or $60+. In every other case Ipoker will rake more than Full Tilt.
Assuming 6-handed game:
$16 pot. Ipoker rakes 80c, Full Tilt Rakes nothing.
$32 pot. IPoker rakes $1.60, Full Tilt Rakes $1.
$48 pot. Ipoker rakes $2.40, Full Title Rakes $2.
This change means IPoker are pretty much always making more rake. especailly in the smaller pots (Raise/Call/Bet Fold style).
super Short it's slightly different at FT starts raking in 50c increments rather than $1 increments but it's still better that Ipoker. Bascially Flat % rates are pretty much the worst way for the player to be paying rake. Stars and Full Tilt both have "Step" structures and they're better for the player.