Please post the URL to your gallery so that I can take a look at the configuration options that you are using.
I created a test gallery using the following configuration settings (to try to replicate what I see in your first screenshot) with all other settings at their default values.
The thumbnails were vertically centered against the main image.
I then increased thumbRows to 9 and the thumbnails were still vertically centered against the main image.
SimpleViewer Support Team