Do not immediately re-queue repeating tasks, or they may simply keep repeating on this tick, until the 35ms time limit runs out.

src/main/java/org/bukkit/craftbukkit/scheduler/CraftScheduler.java

@@ -49,6 +49,7 @@ public class CraftScheduler implements BukkitScheduler, Runnable {
             long firstTick = -1;
             long currentTick = -1;
             CraftTask first = null;
+            TreeMap<CraftTask, Boolean> nextQueue = new TreeMap<CraftTask, Boolean>();
             do {
                 synchronized (schedulerQueue) {
                     first = null;
@@ -64,7 +65,7 @@ public class CraftScheduler implements BukkitScheduler, Runnable {
                                 processTask(first);
                                 if (first.getPeriod() >= 0) {
                                     first.updateExecution();
-                                    schedulerQueue.put(first, first.isSync());
+                                    nextQueue.put(first, first.isSync());
                                 }
                             } else {
                                 stop = true;
@@ -78,6 +79,10 @@ public class CraftScheduler implements BukkitScheduler, Runnable {
                 }
             } while (!stop);
 
+            synchronized (schedulerQueue) {
+                schedulerQueue.putAll(nextQueue);
+            }
+
             long sleepTime = 0;
             if (first == null) {
                 sleepTime = 60000L;