Local install of live site looks different Localhost site looks different than live site. 

Drupal 7.37 > 7.5 (Commons), viewed in Chrome on Mac OS X. 

Prep Steps:


installed a clone of the website from an outdated repository on my local machine
reconciled the code differences between the live site and the slightly outdated repository site
imported a current copy of the database from the live site. 
featurized database configurations
updated most of the modules as well as Drupal core. 
checked default theme and settings to make sure they are the same between sites


After noticing the problem:


downloaded theme files into respective locations
installed stage_file_proxy on local dev to load any files I ignored


Thematic Differences

From the moment I imported the database, until now, after all updates have been performed, there is a thematic difference between the live site and my local version. (The difference is slight, but annoying.) 


live site is centered and contained, local stretches all the way across in some places but stays left aligned in others
some fonts are larger on local site
navigation menu splits itself to a new line early
live site has blocks on the right, local has one column with blocked content at bottom


Summary of Question

Is this a commonly known problem when certain steps are forgotten and is there another place to address configuration besides in the codebase and the database or is this probably not a theming issue but something else?

Update: I pushed the site up to my remote dev server anyways, to see if the problem was environmental or database and codebase. The remote dev looks perfect. There is definitely an issue with my local dev environment causing this somehow.
Sounds like some CSS files are not loaded on the local site. Or some additional or other CSS files are loaded on the local site.
Clear caches
First thing to start troubleshooting the local site is to clear the caches. Not only CSS/JS caches but all caches.
If the site has the Advagg caching module installed, then sometimes it is not enough to clear its cache by clicking the Administration menu link. Advagg cache might also need to be cleared by clicking the Flush AdvAgg Cache button on this path:  /admin/config/development/performance/advagg/operations
If the above does not help then on the same Advagg page there are more buttons to click, hidden behind the headings containing 'Clear' and 'Delete'.
Look at CSS with Firebug
Firebug is an addon for Firefox. Instead of this you can also use the browsers built in inspector by pressing F12(maybe another key on Mac).
See what CSS is different and if the CSS is taken from different files on live site vs local site.
Panels Page layout
Having blocks on the right vs bottom could also be affected by Panels Page layout. Check for that if the blocks are still wrong after you got all other thematic right by getting all CSS right.