One problem related to transmission noise has been reported for the 1999 Mazda Miata. The most recently reported issues are listed below.
Loud noise from transmission in 4th gear from 3500 - 4000 rpm at full throttle. Mazda claims this is normal and after driving 10 seperate 99 Miata's this noise is not normal. The noise is present on all 99 Miata's but the loudness varies. On my Miata the noise is 2 -3 times as loud as all other 99 Miata's I have driven.