While trying to customise one of the themes from the TenThemesForSharePoint pack I found that whenever I modified and deployed the theme.css file and deployed, the changes did not take effect.

To get the changes to take effect I needed to open the browser, navigate to the sharepoint site, then go to Site Actions > Site Settings > Site Features and then Deactivate the theme, and then Re-Activate it. The new theme.css would then be applied. Additionally, sometimes I would need to press the Refresh button on the browser!