Your file has 5 channels, which led to a sample peak above 1.0. This is now fixed by downmixing to stereo before the peak calculation. However since this is very unusual, I am not sure how players handle replaygain with tracks having more than 2 channels. All it takes is a difference in the downmixing algorithm and the volume will be off.
TTA files can have ID3 and/or APE tags. Previously r128gain was always adding ID3 for TTA files, but since your sample file only has APE and no ID3, it seems more logical to reuse the APE tags in that case.
http://sss.chaoslab.ru/08%20-%20Pittsburgh%20Symphony%20Orchestra;%20Manfred%20Honeck,%20music%20direct%20-%20Allegro%20con%20brio.dff.tta.tta
sample of not handled file.