I'm going to assume that you are adding this in the user stylesheet in the Preferences/Styles for the viewer. Hyphens: auto may not be supported but have you tried the other hyphen options used by various renderers? Or adding !important to the end of the line?
Here's what one poster gave as his hyphenation options:
Code:
adobe-hyphenate: auto !important;
-webkit-hyphens: auto !important;
-moz-hyphens: auto !important;
-ms-hyphens: auto !important;
-epub-hyphens: auto !important;
hyphens: auto !important;