I was having the issue where some of the attack hit effects were played much later than they should be. I busted out my old boxed copy and found that the sound effects play just when they should on it. The movies don't work well on that version though. Then I figured I would try using the patch 1.04 on the GOG version, even though its already patched. It seems to have worked. No guarantees it will work for you, but its worth a try.

1.04 patch can be found here:
[url=http://student.fnm.uni-mb.si/~avisnikar/septerra/patch/PatchIndex.php]http://student.fnm.uni-mb.si/~avisnikar/septerra/patch/PatchIndex.php[/url]

Its another EXE file to use instead of the one you already have.

Edit:
This solution seems to be imperfect. After more playing I found that some dialog will end early. So by fixing one problem I seem to have created a bigger one.