You could check if you've enabled all the proper graphical options (through FSO Settings), your options might not have been applied to the new build you've downloaded.
Also look into whether all the FSPort, MediaVPs and fsport-mediavps packages are enabled via the Modify option.
And maybe you've got some strange lighting settings applied?
Eventually you could post a screenshot of the graphical issues you see. Also you could use the Lab (F3 in main menu) to view all models and weapon effects, it'd make taking a screenshot of the problem easier. You might have to need to select a background before loading models/effects, though.