Basically there's more offset on many newer 29er forks (around 45-52mm) to account for a slacker HA (eg 70-71 ish compared to early 71.5~72 degree bikes) that avoids your weight being too far fwd or the front-centre being too short compared to the often-long rear centre, a common complaint of early 29ers. More offset also keeps trail from getting too long on bikes with a slacker HA.
But there's no solid reason in this since a bit slacker-still HA with less fork offset (around 40-45mm) gives a similar trail figure and similar relationship between bar, BB and front axle. ie What comes first, offset, trail or HA? )
41mm rake can still work fine, if you wanted less trail (lighter steering at expense of some stability) just add a longer-offset fork. Maybe not on a 2006 29er, i guess the HA's closer to 72 than 70?
There's sod all wrong with a 72 HA / low offset fork on a 29er BTW, there's many being ridden and well-rated now with that kind of front end. So your current set-up may well be fine, just down to whether it's ok for you or not.