When I ran the retest, I realised that I had forgotten to run winecfg before installing my app the first time. However, repeating the test WITH running winecfg before installing the app led to my old bugs occurring as in earlier wine versions.
My questions then are:
1) Should winecfg still be run before installing the first app (to create the .wine directory etc.)?
2) If this hasn't changed, then how on earth am I getting better results by doing it incorrectly (and what's the best thing to do about it)?!?

Standard procedure I used for installing the app (very simply):
a) Delete old .wine directory
b) Run winecfg (which I forgot the first time)
c) Run setup.exe
d) Run app
e) Test
f) Repeat steps a-e for retest.
The main bug that smacked me in the face (or rather didn't) was 8460 to do with Tahoma font and "Invalid Floating Point Operation"s.
Stuart