Volume Overlay Displaying Incorrectly/Not Centered
I would try a few things.


Check if BezelUIServer is running constantly (in Activity Monitor). It should only start (for short durations) whenever you display an overlay (called Bezel by Apple). That server is actually located here:
/System/Library/LoginPlugins/BezelServices.loginPlugin/Contents/Resources/BezelUI/BezelUIServer
If you can download the OS X Installer, you might be able to extract the specific "LoginPlugin" from the installation disk and overwrite it (with an admin account) under: /System/Library/LoginPlugins/BezelServices.loginPlugin
There appears to be a configuration file com.apple.BezelServices.plist under /Library/Preferences. You might want to reset this file (just rename it and see if OS X just re-creates it for you).
Attach a secondary monitor and make that your primary screen (with both displays setup side-by-side and not to mirror). This way you might see if the overlay is also misplaced on the secondary screen in the same location. It might have something to do with your graphics card (settings) and you might get a different result if that has to display two monitors.
Also run Disk Utility and to Verify Disk Permissions then Repair Disk Permissions and also Verify Disk and Repair Disk if necessary, but this may require you to log in from a recovery partition.
If nothing works and you really want this fixed, you could reinstall OS X, but you should really backup your files for this one. Well, in your case with the MacBook acting up, I would do that in any case! There is a very simple step-by-step guide from Apple here: https://support.apple.com/kb/PH18872 and it goes like this:



  
  In the menu bar, choose Apple menu > Restart. Once your Mac restarts (and the gray screen appears), hold down the Command (⌘) and R keys.
  Select Reinstall OS X, then click Continue.
  Follow the onscreen instructions. In the pane where you select a disk, select your current OS X disk (in most cases, it’s the only one available).