DOHHHHHHH
My comment was right: "and next is not fading"
but you don't do that with !sines[i + 1].done()
Spot the sneaky error? maybe I should have said "and next is done fading" 8)
Try: (left the debug in but I'll guess you know how to remove that ![]()
#include <FadeLed.h>
//91 step sine table 0 = 0 degree, 90 = 90 degree
const flvar_t SineTable[91] PROGMEM = {
 0, 4, 9, 13, 18, 22, 27, 31, 35, 40,
44, 49, 53, 57, 62, 66, 70, 75, 79, 83,
87, 91, 96, 100, 104, 108, 112, 116, 120, 124,
127, 131, 135, 139, 143, 146, 150, 153, 157, 160,
164, 167, 171, 174, 177, 180, 183, 186, 190, 192,
195, 198, 201, 204, 206, 209, 211, 214, 216, 219,
221, 223, 225, 227, 229, 231, 233, 235, 236, 238,
240, 241, 243, 244, 245, 246, 247, 248, 249, 250,
251, 252, 253, 253, 254, 254, 254, 255, 255, 255,
255};
//Make FadeLed object with a sine lookup table of 91 (0 to 90 including)
FadeLed sines[3] = {{3, SineTable, 90}, {5, SineTable, 90}, {9, SineTable, 90}};
const byte NrSines = sizeof(sines)/sizeof(sines[0]);
void setup(){
 Serial.begin(115200);
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 for(byte i = 0; i < NrSines; i++){
  sines[i].setTime(1000); //halve period, 0% to 90% or 90% to 0%
 }
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 for(byte i = 0; i < NrSines; i++){
  sines[i].beginOn();
  delay(1000);
  sines[i].begin(0);
 }
 //start the first
 sines[0].on();
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 Serial.println(NrSines);
 Serial.println();
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 for(byte i =0; i < NrSines; i++){
  Serial.println(sines[i].get());
  Serial.println(sines[i].getCurrent());
  Serial.println(sines[i].done());
  Serial.println();
 }
}
void loop(){
 FadeLed::update();
 for(byte i = 0; i < NrSines; i++){
  //for all but last (who has no next)
  if(i < (NrSines - 1)){
   //if >50% (45 degree) and next is not fading and is off
   if((sines[i].getCurrent() >= 45) && sines[i + 1].done() && (sines[i + 1].get() == 0)){
    sines[i + 1].on();
   }
  }
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  //if sin is 100% (90 degree), fade back down
  if(sines[i].done() && sines[i].get()){
   sines[i].off();
  }
 }
}