This is true. If your have read John Palmer's book, you might recall him going over this in chapter 5.
I don't know the recipe but it sounds like you are boiling hops and water for 60 minutes and adding DME at 5 minute versus hops and DME for 60 minutes.
The question is how much it affects the IBU and if it can be detected, so it is worth it?
For this example, I have 1 oz of Amarillo Gold at 10%aa
This gives me a total of 10 AAU
10lbs DME at 1.073 gravity
John's calculation using the Tinseth formula is as follows
Example 1 - DME all at 5 minute
IBU(60) = 10 x .36 x 75 / 5 = 54 (.36 is the approx % of hop utilization in water)
IBU(1) = 10 x .04 x 75 / 5 = 6 (.04 is the approx % hop utilization of 1.073 wort for 5 minutes)
total IBU = 60
Example 2 - DME 60 minutes
IBU(60) = 10 x .196 x 75 / 5 = 29.4 (.196 is the approx % hop utilization of 1.073 wort for 60 minutes)
So, yea, the math says it makes a difference. Beersmith 1.4 seems to use the hop boil time and total estimated gravity.
There are other reasons to only boil the hops with wort and for longer times.