There is a strange thing that the Sitecore Update Installation Wizard does for Standard Values items when it installs them in a Sitecore Update Package.
For __Renderings and __Final Renderings fields, if you have reset the value (made it null) of one of those fields in your Standard Values item in the package...the Installation Wizard still won't make your instance reflect this.
Even with the field reset (so the raw value doesn't exist...i.e is null)...the Update Installation Wizard treats the Standard Values in a special way, and won't actually make your target Sitecore instance reflect that change. (Even with settings like TDS's 'AlwaysUpdate'). Instead, the installer checks if the Sitecore value is not null, and then it keeps THAT value....not the null value that your package contains.
This is a frustrating feature of Sitecore's Installation Wizard, that I can only imagine is an attempt to prevent overwriting of content.... but it definitely gets in the way when you use something like TDS, and know exactly what you want it to do.
To get around this issue, you can either manually reset the field's Standard Values after the deployment.... or, if using TDS, write a Custom Post Deploy Step that would reset the specific field. http://www.teamdevelopmentforsitecore.com/en/blog/creating-tds-custom-post-deploy-step