Hello,
I have two masters and serif components, but when I rotate them by 90degrees they are not visible in interpolated instances. They are visible in preview panel of Glyphs, but in exported otfs.
Why is that?
Rotated the same in all masters?
Perhaps flipped in one master?
Path direction?
Two components on top of each other?
Have you checked the outline compatibility of all serifs in all masters? Different starting points? Different path directions?
If all of this was no help, please send us the file. 
I just made a new file with 2 masters, than created A, ogonek and Aogonek, rotated by 90deegree A components in Aogonek glyphs and after exporting, in Aogonek (Ą) there is only ogonek moved to the top of the glyph.
If I rotate by a value in a range 0-90degree the component is scaled down.
Maybe a bug of version 1.3.19 (471) ?
I sent a file.
Fixed it. Thanks for the file.