Does that make any sense to anyone? And does anyone know of a way to change it?
From the sounds of it, you have one or both of the "Stroke In" and "Stroke Out" options selected -- these add a taper to the beginning and end of your strokes regardless of the pressure settings of your tablet and the actual pressure you're applying when you draw:

If you uncheck these options, then the stroke you draw should accurately reflect the pressure settings and the pressure you apply.
Also be aware that the way the pen/brush behaves as you apply pressure can also be customised within MS. Click the green button in the Tool Options palette:

to bring up an editable curve that controls the pressure response:

TBH, this curve could be larger but you can add extra points to it just by clicking on it, and each point can then be dragged. You can leave this dialogue active while you draw, so you can tweak the curve, try a couple of strokes to see how they work, then tweak some more if you're not happy.
I won't pretend that there isn't a learning curve here -- this isn't Photoshop, it's a package that seems to have been clearly designed by people who know about drawing comics, for people who want to draw comics. A lot of it seems quite counter-intuitive, but that's because people have become used to adapting their workflow to Photoshop, which tries to be all things to all artists, photographers and designers.
I've just mastered the panel cutter, which is fantastic, but which does take some getting your head around. Perspective snap (which requires the full EX version) is just awesome. Drop a perspective (1, 2 or 3 point) ruler onto your document, move the vanishing points as you see fit, and then every line you draw will snap to the closest line on the perspective grid
as you draw it. Skyscraper in three point perspective in minutes.
Your linework layers (as PJ points out) stay in aliased bitmap mode, but you can add grayscale or colour layers to it without ever having to change the document's colour mode.
It's a good bit of kit. PJ is doing some great work with it ... I'm wondering if we shouldn't start a "Let's all figure out Manga Studio together" thread where we can go through stuff as we work it out?
Cheers!
Jim