I have the same problem.  Basically, here is my setup, my experience,
my trouble-shooting, and my observations.  I think I'm on the right
track...but I don't yet know how to solve it.

My Setup
- Outlook 2003
-- Set to Tools|Options|Mail Format| of 'Use Word to edit email' and
'Use Word to read RichText messages'.  [AN IMPORTANT POINT, as you'll
see below.]
-- Default email composition type is set to HTML
- Word 2003

My Experience
All was well, with my email reading and writing, related to appareent
font size (zoom), until I changed the zoom within a Word document.
That's when it all turned sour.  From then on, when viewing RichText
emails, the text would show up as puny.

To temporarily alleviate that, within the email message I was viewing,
I would got to View|Zoom| and change it to 100%...from 62%.  Why was
it set at 62%?  I have no idea, other than that perhaps it was a
remnant of my having changed the zoom settings in the aforementioned
Word document at one time.

I later found that, IF I HAD READ A RICHTEXT EMAIL, THAT SHOWED UP
SHRINKY, THEN ANY CREATE-NEW MESSAGES I OPENED WOULD ALSO BE SHRINKY.
Annoying to say the least.

So, being a good little IT'ish boy, I went into Outlook's options,
disabled the 'Use Word' features, exited all Outlook windows, went
into the Task List and killed any remaining Outlook or Word processes
(often needed, since both of them like to linger around back-stage
after the show), re-launched Outlook, and saw what I could see.

In this new scenario -- only using Outlook -- all messages that I read
are displayed at the expected, normal zoom size.  All new messages I
create are displayed at the expected, normal zoom size.

My problem is that I really like Word's functions, in the email
editor.  The ability to convert plain text, to HTML, is a function I
use a lot, because I like to reply to folks with highlighting,
bolding, or other formatting.  That is not available, via Outlook, but
is only available when using Word as the editor.

When I change back, to using Word again, the problems re-appear.  And,
I have tried various combinations of the Word options, such as only
turning on one or the other of the two options.

I believe the problem is not specifically an Outlook problem, but
rather, it has something to do with the state in which Word itself was
left, after I viewed that original Word document using whatever
zooming changes I made.

So, I went into Word docs, zoomed them all to 100%, saved the
documents, exited Word...but to no positive effect, related to the
Outlook problem of this posting.  My next step will be to investigate
if there is some Word cache I can clear out, some settings I can
reset, etc.  However, I WORK for a living...so when I get to it will
be another matter.

The search continues....