Known problem. The subrepo in your second example is pulled from
main/nested, because the pull source is not being propagated down to the
subrepo code.

Tested with Mercurial V1.4.3 on Suse Enterprise Server 10.2

In case of a master repo 'main' with a nested repo 'nested'. If we clone
that 'main' to 'main2', it is possible for main2 to pull from main1 but not
the opposite.

First way (it works) :
hg init main
cd main
hg init nested
echo test > nested/foo
hg -R nested add nested/foo
echo nested = nested > .hgsub
hg add .hgsub
hg ci -mtest
cd ..
hg clone main main2
cd main
echo modification > nested/foo
hg ci -mmodif
cd ..
cd main2
hg pull ../main
hg update

Second way (it doesn't work) :
hg init main
cd main
hg init nested
echo test > nested/foo
hg -R nested add nested/foo
echo nested = nested > .hgsub
hg add .hgsub
hg ci -mtest
cd ..
hg clone main main2
cd main2
echo modification > nested/foo
hg ci -mmodif
cd ..
cd main
hg pull ../main2
hg update