disable-fastledshow.diff

--- wonky-timer.ino     2016-10-30 13:53:06.501195684 -0700
+++ wonky-timer.nofastled.ino  2016-10-30 13:53:44.877448425 -0700
@@ -30,14 +30,14 @@
 void blinkRed() {
     leds[0] = CRGB::Red;
     log("before red  ");
-    FastLED.show();
+    //FastLED.show();
     log("after  red  ");
 }

 void blinkBlack() {
     leds[0] = CRGB::Red;
     log("before black");
-    FastLED.show();
+    //FastLED.show();
     log("after  black");
 }

Output_with_FastLED.show()

Starting firmware.                    
before red   0  19668  ls:19668  r: 19668  b: 20668    Sun Oct 30 20:49:56 2016
after  red   0  35790  ls:19668  r: 19668  b: 20668    Sun Oct 30 20:49:57 2016
before black 0  20668  ls:20668  r: 21668  b: 20668    Sun Oct 30 20:49:57 2016
after  black 0  55460  ls:20668  r: 21668  b: 20668    Sun Oct 30 20:49:58 2016
before red   1  21668  ls:21668  r: 21668  b: 22668    Sun Oct 30 20:49:58 2016
after  red   1  56460  ls:21668  r: 21668  b: 22668    Sun Oct 30 20:49:59 2016
before black 1  22668  ls:22668  r: 23668  b: 22668    Sun Oct 30 20:49:59 2016
after  black 1  57460  ls:22668  r: 23668  b: 22668    Sun Oct 30 20:50:00 2016
before red   2  23668  ls:23668  r: 23668  b: 24668    Sun Oct 30 20:50:00 2016
after  red   2  58460  ls:23668  r: 23668  b: 24668    Sun Oct 30 20:50:01 2016
before black 2  24668  ls:24668  r: 25668  b: 24668    Sun Oct 30 20:50:01 2016
after  black 2  59460  ls:24668  r: 25668  b: 24668    Sun Oct 30 20:50:02 2016
before red   3  25668  ls:25668  r: 25668  b: 26668    Sun Oct 30 20:50:02 2016
after  red   3  60460  ls:25668  r: 25668  b: 26668    Sun Oct 30 20:50:03 2016
before black 3  26668  ls:26668  r: 27668  b: 26668    Sun Oct 30 20:50:03 2016
after  black 3  61460  ls:26668  r: 27668  b: 26668    Sun Oct 30 20:50:04 2016
before red   4  27668  ls:27668  r: 27668  b: 28668    Sun Oct 30 20:50:04 2016
after  red   4  62460  ls:27668  r: 27668  b: 28668    Sun Oct 30 20:50:05 2016
before black 4  28668  ls:28668  r: 29668  b: 28668    Sun Oct 30 20:50:05 2016
after  black 4  63460  ls:28668  r: 29668  b: 28668    Sun Oct 30 20:50:06 2016
before red   5  29668  ls:29668  r: 29668  b: 30668    Sun Oct 30 20:50:07 2016
after  red   5  64460  ls:29668  r: 29668  b: 30668    Sun Oct 30 20:50:07 2016
before black 5  30668  ls:30668  r: 31668  b: 30668    Sun Oct 30 20:50:08 2016
after  black 5  65460  ls:30668  r: 31668  b: 30668    Sun Oct 30 20:50:08 2016
before red   6  31668  ls:31668  r: 31668  b: 32668    Sun Oct 30 20:50:09 2016
after  red   6  66460  ls:31668  r: 31668  b: 32668    Sun Oct 30 20:50:09 2016
before black 6  32668  ls:32668  r: 33668  b: 32668    Sun Oct 30 20:50:10 2016
after  black 6  67460  ls:32668  r: 33668  b: 32668    Sun Oct 30 20:50:10 2016

Output_without_FastLED.show()

Starting firmware.
before red   0  20848  ls:20848  r: 20848  b: 21848    Sun Oct 30 21:02:27 2016
after  red   0  20848  ls:20848  r: 20848  b: 21848    Sun Oct 30 21:02:27 2016
before black 0  21848  ls:21848  r: 22848  b: 21848    Sun Oct 30 21:02:28 2016
after  black 0  21848  ls:21848  r: 22848  b: 21848    Sun Oct 30 21:02:28 2016
before red   1  22848  ls:22848  r: 22848  b: 23848    Sun Oct 30 21:02:29 2016
after  red   1  22848  ls:22848  r: 22848  b: 23848    Sun Oct 30 21:02:29 2016
before black 1  23848  ls:23848  r: 24848  b: 23848    Sun Oct 30 21:02:30 2016
after  black 1  23848  ls:23848  r: 24848  b: 23848    Sun Oct 30 21:02:31 2016
before red   2  24848  ls:24848  r: 24848  b: 25848    Sun Oct 30 21:02:31 2016
after  red   2  24848  ls:24848  r: 24848  b: 25848    Sun Oct 30 21:02:32 2016
before black 2  25848  ls:25848  r: 26848  b: 25848    Sun Oct 30 21:02:32 2016
after  black 2  25848  ls:25848  r: 26848  b: 25848    Sun Oct 30 21:02:33 2016
before red   3  26848  ls:26848  r: 26848  b: 27848    Sun Oct 30 21:02:33 2016
after  red   3  26848  ls:26848  r: 26848  b: 27848    Sun Oct 30 21:02:34 2016
before black 3  27848  ls:27848  r: 28848  b: 27848    Sun Oct 30 21:02:34 2016
after  black 3  27848  ls:27848  r: 28848  b: 27848    Sun Oct 30 21:02:35 2016
before red   4  28848  ls:28848  r: 28848  b: 29848    Sun Oct 30 21:02:35 2016
after  red   4  28848  ls:28848  r: 28848  b: 29848    Sun Oct 30 21:02:36 2016
before black 4  29848  ls:29848  r: 30848  b: 29848    Sun Oct 30 21:02:36 2016
after  black 4  29848  ls:29848  r: 30848  b: 29848    Sun Oct 30 21:02:37 2016
before red   5  30848  ls:30848  r: 30848  b: 31848    Sun Oct 30 21:02:37 2016
after  red   5  30848  ls:30848  r: 30848  b: 31848    Sun Oct 30 21:02:38 2016
before black 5  31848  ls:31848  r: 32848  b: 31848    Sun Oct 30 21:02:39 2016
after  black 5  31848  ls:31848  r: 32848  b: 31848    Sun Oct 30 21:02:39 2016

wonky_timer.ino

// allow SYSTICK interrupt to fire
#define FASTLED_ALLOW_INTERRUPTS 1
// This #include statement was automatically added by the Particle IDE.
#include "FastLED/FastLED.h"
FASTLED_USING_NAMESPACE;

// How many leds in your strip?
#define NUM_LEDS 12
#define DATA_PIN 3

// Define the array of leds
CRGB leds[NUM_LEDS];

int count = 0;
long loopstart, millis_after_show, redtime, blacktime; // loopstart is the time each loop starts
String msg;

#define BLINK_INTERVAL 1000

void log(String color) {
    msg = String(count) + "  " + String(millis()) + "  ls:" + loopstart + "  r: " + redtime + "  b: " + blacktime + "    " + Time.timeStr();
    Serial.println(color + " " + msg);
}

void pauseAndLog(String color, int numPause = 1, int duration = 1000) {
    log(color);
    for(int i = 0; i < numPause; i++) {delay(duration);}
}

void blinkRed() {
    leds[0] = CRGB::Red;
    log("before red  ");
    FastLED.show();
    log("after  red  ");
}

void blinkBlack() {
    leds[0] = CRGB::Red;
    log("before black");
    FastLED.show();
    log("after  black");
}

void setup() {
    Serial.begin(115200);
    delay(15000);
  	FastLED.addLeds<NEOPIXEL, DATA_PIN>(leds, NUM_LEDS);
    Serial.println("Starting firmware.");
    loopstart = millis();
    redtime = loopstart + BLINK_INTERVAL;
    blacktime = redtime + BLINK_INTERVAL;
}

void loop() {
    loopstart = millis();
    if(loopstart >= redtime) {
        blinkRed();
        redtime += 2 * BLINK_INTERVAL;
    }
    if(loopstart >= blacktime) {
        blinkBlack();
        blacktime += 2 * BLINK_INTERVAL;
        count++;
    }
}