Two modifications have been made to the MHX importer.
First, the files were moved from
utils/mhx/ to
importers/mhx/blender249/. The utils folder is not included in the A4 release, and thus neither was the MHX importer. With the new file structure, it is clear where to put MHX importers for other packages (e.g. Blender 2.5), as well as importers for other formats that we might want to define in the future (e.g. mhx2). The importers directory should be included in the next release (note to Manuel and Joel).
Second, FK/IK switch has been brought back as an option, despite it being buggy. Let me describe the problem, in the hope that some Blender guru can explain how to fix it.
When we

run the mhx_import script, the toggle button
FK/IK switch decides whether dynamical switching is possible. If not, we have two more buttons to set
Arm IK and
Leg IK; they have no effect if the FK/IK button is active

. Let us load a character with switching enabled. We now set the amount of IK with the four sliders on the top of the panel (left/right and arm/leg). The character has two sets of arms; the IK bones and the deform bones

, which have a Copy Rotation constraint driven by the slider bones. The setup is best explained by a picture. If you move the slider bones, the deform bones should move towards the bones in the IK chain, but they don't. However, once the mouse is clicked inside the constraint area in the buttons panel, the influence is suddenly updated and the deform bones snap into place. Sometimes. But sometimes they don't.
So this is the problem with FK/IK switching. If somebody knows how to make this work properly, only using Python, I would be happy to know.

Update: Bruno Chansou has found an explanation for the behavior on another forum. The constraint IPOs are connected to a pose action rather than to the constraints themselves (at least that is what the tooltips say). To fix it, do the following:
1. Select the bone LoArm_L
2. Click on the Copy Rotation constraint. The driver IPO curve appears in the IPO window. It is called "CoIpo.001".
3. The circled button is pressed. Unpress it.
4. When the button is unpressed, the IPO curve disappears. Reselect it in the popup menu to the right of the button. Make sure to reselect the correct curve (CoIpo.001), because otherwise the constraint may be driven by the wrong bone.
5. Repeat for all other driven bones.
The only problem with this approach is that there are 14 different bones with driven constraints, and you must repeat the procedure for each of them. To fix this manually after import is doable, but it would be better if the import script could handle it. So is there some way to unpress the button (disconnect the IPOs from the pose action) from within Python?
The affected bones are: UpArm_L, LoArm_L, Hand_L, UpLeg_L, LoLeg_L, Foot_L, Toe_L and the same on the right side. Some Limit Distance constraints are affected too, but that is a bug which will soon be removed.
Update 2: Bruno pointed out that the IK influence is also updated if you click in an Ipo or action editor window. Unlike clicking the the buttons window, this updates all influences in a predictable manner. Perhaps this is the best way to proceed if you don't want to spend time reconnecting all ipo curves for your character.