When receiving absolute frames with big (>0xffffff) timestamps an error used to occur because RTMP type 3 chunks carry absolute timestamps. That's undocumented feature which I have implemented long ago. However that was not properly tested.
I want to thank people who helped me with fixing that and provided detailed responses about publishing from FMLE. In 0.8.2 version that was completely fixed. Now nginx-rtmp has full support of long publishing from Adobe products.