Try:
[nggallery id=1 template=caption]
Update: So basically my effect is not working on my homepage when using do_shortcode but everything works correctly when using a the standard shortcode on a page.
Any ideas why it would work differently using do_shortcode when this method worked flawlessly prior to the 3.0 and NG 1.5.5 upgrade?
Try using:
[nggallery id=1 template=caption]