i am seeing this exact same issue. running ST 3.2 on macOS 10.13.6. once i upgraded from ST 3.1 (Build 3170) to ST 3.2 (Build 3200) all of my icons for PHP, CSS, XML, JS files are now generic blank document icons. i tried removing and reinstalling ST 3.2 but no dice. the file associations are still correct (these files still open with ST) but the old file icons are now gone. any help appreciated. thanks.