Thread And Clock Management

I have objects (baddies in a game) that have individual clocks/counters assigned to them (when I make an object, I fill an integer based array list with a new digit entry at a value of one) that all happens in threads. then in another thread, I am checking the whole list of clocks, to see if any are equal to a wanted value , then I am taking an action and reseting the clock at that point on the array list.

now, the problem is:even though my code says " yes, I've taken that action because the value of array position x was >= specified value and I will now reset the clock" it doesn't reset the clock. Here is what it looks like

*these are excerpts taken from a really big program, however they should stand on their own as they are individual classes

Java Code:

public class levelclock extends Thread {
public void run() {
while (Run2 == true) {
if (Run == false) {
try {
Thread.sleep(100);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();

[code]....

(Attached, just open up the zip and read the .txt)