I've seen that happen a lot as well. What I've also discovered recently is that inspite of the fact that question elements are a set of "grouped" objects, you can still select the text box for the question text. It's sometime a bit hard to do, but here's the point:
(PS: I'm still using PPT 2003, but the same can be achieved w/ PPT 2007)
When you have the question text box selected (all around the text object you should see a set of circles with little X's in them), click on Format from PowerPoint's main menu and trace down and select "Format". When that dialog box opens, click on the Text tab...from there what you should see is the vertical alignment set to "middle"...that's the default, but you can change it to "top" and that, I think, shoud help w/ your alignment issue with the questions.
Thanks for the tip...it got me on the right track. (I'm using PPT 2003. )
The text alignment didn't seem to work for me, but this did:
Click the text field (as you described) to get the X's.
Right-click and select Format Text Box.
Play with the internal margin with for the text box to get the alignment correct. (For example, I changed the bottom margin to 0.4").
What's weird is that the bottom margin adjustments were not consistent from slide to slide (for example, on the first question, I only needed
to change the bottom margin to 0.2), but my quiz looks way more acceptable now.