The simplest way is...
Open Windows registry, find key
Now you can change
The default is 2 (possible points, but I don't sure), but you can change it (0 - to delete all paddings).
BUTdon't forget to process all your equations (after PicturePadding was changed) in Word (by Format) or in InDesign (by Batch convertion... - it's possible if you use MT-Script for InDesign (www.mtscript.ru))
And only after that you will see equations without paddings.