varnish is not evenly applied. That is, the darker grain seems
to repel the varnish, whereas the lighter areas have taken the
varnish no problem.

You must rub down with a fine sandpaper between coats (no coarser than 150
grit). I tend to run down the first coat and the penultimate coat using an
orbital, which I find tends to leave less marks than other methods. I
usually put on a very thick first coat and rely on the sander to flatten off
the high bits.

Christian.