Its name starts with A, so i assume those programs picks the first available font. Even if it seems silly, it could be seriously the culprit.
Also neither Caligra nor Trojita are native programs thus they dont respect any Appereance preferences, because you know, GNU is not about consistency, and the porters (in case of Trojita: its me) are uneducated niemands, so we are happy the program does something at all not just crashing. Please join us and fix our ports. Thanks!