What is the biological difference in a growing male vs. female fetus and what 
have doctors/psychiatrist's found about boys vs. girls personality traits that 
are not learned but gene based?

Although a fetus’s genetic sex is determined at conception by either the 
presence of a Y chromosome or a second X chromosome, physiological differences 
do not begin to emerge until the formation of sex organs after 6-7 weeks.  The 
testes of a male fetus generate two kinds of hormones which influence the 
development of the reproductive system: Mullerian Inhibiting Substance, which 
prevents the formation of female Mullerian ducts (the uterus and fallopian 
tubes), and androgens which stimulate the growth of the male Wolffian ducts.  

Here is a description of the process of sex differentiation in fetuses:
http://www.hopkinsmedicine.org/pediatricendocrinology/intersex/sd2.html

If you’re interested in the behavioral differences between males and females, 
you may want to read “Brain Sex”, a book by Anne Moir, Ph.D. and David Jessel, 
which talks about the differences between males and females, and specifically 
the effects of different hormones on the development of the human brain.  
Although the behavioral differences caused by different brain development are 
not entirely clear, it is clear that there are differences in the central 
nervous system between males and females, which are caused by the presence of 
hormones during development.  Aggressiveness is thought to be one behavioral 
trait influenced by gender differences in the development of the brain.  Here 
are some web sites that discuss the differences in the brain and development of 
the central nervous system due to gender:

“Development of the Cerebral Cortex: XV. Sexual Differentiation of the Central 
Nervous System” by Roger A. Gorski, Ph.D
http://www.med.yale.edu/chldstdy/plomdevelop/development/March99.html

Male-Female Differences – BrainPlace.com
http://www.brainplace.com/bp/malefemaledif/default.asp

I hope this answers your question!

A somewhat tangetial, but interesting and oft overlooked fact:

The XY model of sex-determination is mammal specific.  A number of
other models are used by other animals (and plants, but I know little
about them).

Birds use a "WZ" model, which is a mirror image of the mammalian XY
model.  Females birds have one W chromosome and one Z, and male birds
are ZZ.

In crocodiles (and a number of other reptiles), the temperature at
which the eggs are incubated determines their sex: the lower the
incubation tempature, the more females there are, the higher, the more
males.

Fish and non-vertebrates can be even less like us.  Some fish start
their life as females and later become males.  Many invertebrates are
both male and female.  A seperation of genders into different
individuals roughly correlates with complexity.  Most complex animals,
like vertebrates, cephalopods (squid and octopods), and insects, have
seperated the genders, a trait called dioecy.  Many simple animals
like clams and flatworms are monoecious (both genders in the same
indiviual).

Among the group of insects which includes ants and bees, fertilized
eggs become females, while males hatch from unfertilized eggs.  This
is important to the evolution of their social structure (which evolved
seperately, but almost identically in bees and ants).

There, not really what was being asked, but interesting, I think.