Tashkeel problem when PDF export

I’m having a problem with the placement of tashkeel (arabic marks) when exporting from old versions of Word to PDF. They look well placed in Word but in the resulting PDF they are not well placed, most of the times happening with alef-ar. I see that this is common to many “recent” typefaces while some that where done with VOLT don’t have that problem. I’m wondering if there is a way to fix this somehow within glyphs, if someone already tried. Probably @khaled ?
Here’s an example on how the kasra-ar and the fathatan-ar get misplaced in the font I’m working on, as well as Greta and Graphik, while in Helvetica works well.