Bi-color visual and two tone audible alert. Need some advice.

This is the first and only code I've ever written so please be gentle. It was written to provide Bi-color (red/green) LED and two tone audible alerts of battery condition. The idea is to conserve as much power as possible.

Known Bug - If an LED is lit when the battery state changes it will stay lit while the other LED blinks. I don't know how to trap this.

Issue - I couldn't get away from delay() completely while using tone(). The code works but I don't know if this is causing the LED bug.

Please advise on what the LED bug might be and/or on how to clean this up, particularly on how to get rid of delay() in the beep function.

/*DTI sketch version 5.0.1
Control code for:
   - Bi-color power LED indication
   - Transmitter selection
   - Audible alerts of transmitter position
   - Audible low battery alert
   - Alert cancel and Alert off functions
Created By Kirk Sceviour
08 Feb 2015
*/

boolean battchange = false; //remains false until PG indicates a change in battery status
boolean powergood = true;  //power supply is good
boolean discard = false; //discard any generated audible alert
boolean noalerts = false;  //alerts are selected on

#define ALERTOFF 13 
#define CANCEL 12
#define TXSEL 8
#define redLED 10 
#define greenLED 9
#define AUDTONE 6
#define SWCOMM 7
#define PG 4


//for blink without delay functions
#define LED_ON 400     //blink interval millis
#define LED_OFF 3000
unsigned long ms;        //time from millis()
unsigned long msLast;    //last time the LED changed state
boolean ledState;        //current LED state

//for beep functions
unsigned long msBeep;    //time from millis()
unsigned long msBeepLast;//last time of beep
unsigned int beepFreq = 440; //frequency of beep
unsigned long beepTime = 200; //duration of beep
unsigned long battBeepPause = 120000; //time between beeps 
boolean audState;     //current audible state

void setup()
{
    pinMode(CANCEL, INPUT); //Cancel button input, mom LOW
    pinMode(ALERTOFF, INPUT); //To Alerts Off switch. LOW = off
    pinMode(TXSEL, INPUT);  //To TXSEL switch. Low indicates COMM 2 selected
    pinMode(redLED, OUTPUT); //Power low indication
    pinMode(greenLED, OUTPUT); //Power good indication
    pinMode(SWCOMM, OUTPUT);//Output to selector IC. HIGH = COMM 2
    pinMode(PG, INPUT); //Normally high, a low indicates poor battery
    pinMode(AUDTONE, OUTPUT); //PWM output pin
    Serial.begin(9600); // for debugging
    int pgValue = digitalRead (4); //for debugging
}
void loop()
{
 msBeep = millis();
 ms = millis();
 noTone(6);


   if (digitalRead(PG) == HIGH)//power good
    {
      blinkgreenLED();
      powergood = true;
    }
    else  
      blinkredLED();
      powergood = false;
      lowbattBeep();
 }
//Beep and Blink without delay functions. All other code above this.

 void lowbattBeep(void)

  {//is it the first indication of low battery?
    if (digitalRead(PG) == LOW && battchange == false) 
      {      
        Serial.print("  first ind  ");
        battchange = true; //change the battery state
      }//was it momentary?
    if (digitalRead(PG) == HIGH && battchange == true) 
        {
         battchange = false; // reset
         noTone(6); //make sure the pin is off
         Serial.print ("  battchange reset  "); 
         }
    if (digitalRead(PG) == LOW)
      { //check time since last beep
      if (msBeep - msBeepLast > (battBeepPause)) 
        {
          tone(6, beepFreq, beepTime); //play
          delay(200);
          noTone(6);
          tone(6, 250, beepTime);//lower tone
          delay(200);
          noTone(6);
          msBeepLast = msBeep;  
        } 
      }
  }

void blinkgreenLED(void)
  {
     //determine the last time the LED was on
    if (ms - msLast > (ledState ? LED_ON : LED_OFF)) 
    {
     //switch states if necessary
        digitalWrite(greenLED, ledState = !ledState);
        msLast = ms;
    }  
  }
void blinkredLED(void)
  {
    if (ms - msLast > (ledState ? LED_ON : LED_OFF)) 
    {
        digitalWrite(redLED, ledState = !ledState);
        msLast = ms;
    }
  }