winisd

The volume you enter is the net internal volume - so no, port displacement, woofer displacement, MDF displacement is not accounted for.

Regardless - woofer displacement would have a negligble sonic impact.

Ur entering a parameter incorrectly...?

What sort of box are you trying to design?  What parameters are you using?  What woofer do you want to use?  Maybe we could be more help...

From WinISD Pro 0.50a7 Help file, under FAQ:

Q. Does WinISD add brace/driver/port displacements to calculated box volume?

A. From Janne Ahonen ( janne@lineateam.org)

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No. WinISD doesn't do guessing, and therefore shows net volume for your box. It would be hard to predict, how you are going to mount your driver. Or the port. Or how much and which kind of bracing you are going to use inside your box. For example, you could mount port completely external to the box, which case "usual" guess would be completely wrong. Bottom line is, that you must calculate and add any displacements by yourself to calculated box volume.

There can be and usually are slight differences in port length equations between the various programs' calculations.  If all is equal in your input from program to program, the differences are so minor that they are in fact neglible (in regard to real-life performance).

In other words, what everybody else said.

Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.

If you are ever designing a box where the difference is noted as "drastic" within less of an inch (1/16th??), you should begin redesigning with a larger port so that the length in fractions of an inch becomes less critical.

A redesign may include changing the actual driver or box type as well as changing the size or shape of the port structure.

If you want a definitive answer to "who is right?", study the fundamental equations used in determining port length  http://www.diysubwoofers.org/misc/portcal.htm  and apply them to your project.

Note:  unless you have used the necessary tools to measure parameters of those Mister Vegas yourself, you are in for some experimentation in designing a vented box, no matter what box type you desire.  In fact, even if you had the woofers measured individually by a lab who specializes in such work, you will still have to allow for experimentation of port design to get the most desirable result.  Cabin (or room) nulls or nodes, cabin / room transfer function, and source material input are some of the factors that will influence the end result. 

Allow for adaptation of port length in your design, at the very least.