I ran into this problem where custom marks (in my case, Armenian punctuation with non-unicode .comb marks) were not combining with their base glyphs. After quadruple checking that .comb glyphs had the correct anchor names and were set as non-spacing marks, I found that having autohint set explicitly to off, either as a custom parameter in the instance or from the export window, would cause the .comb glyph to not attach correctly.
I should also mention that I am noticing this issue when the .comb glyphs have a set width (which automatically reduce to zero on export). However, if I explicitly set the width to zero (which makes it very difficult to select) then the marks are in the correct places.
Version 2.6.5 (1295)