sikuli slows down to a crawl after running for some time

Still not solved

    I tried disabling options in the preference menu. I also tried exiting while loops after a certain count (exit early) in case it was being stuck in a loop and that did not work either. I then decided to write a comment to a file on every section of my program. Nothing abnormal showed up. I though I would see my "could not find egg" message but, the program was working fine as far as code execution order goes. It simply taking too long while doing a search. What could cause this?

The mystery deepens. I put some timers so that I could see where in the program there is a slow down. There is something wrong that happens at the end of the while loop but only after this code has ran hundreds of times. Its really odd because I put the write to file line in the wrong spot so what I end up seeing or rather what I should end up seeing is the same value for the last two print lines. I should be seeing something like .....
      while loop time --> 0.22
      after check position time --> 0.22

But!! as you can see towards the end the "after check position time" takes considerably longer than the "while loop time" YET!!! they happen right after each other. How do you explain that???

    #check if at least one egg exists
    if region1.exists(Pattern("1492966400130.png").similar(0.59),0):
        file.write("FOUND EGG\n") #DEBUG
        foundEggTime = time.time() #DEBUG

        while region1.exists(Pattern("1492966400130.png").similar(0.58),0):
            startWhileTime = time.time() #DEBUG
            file.write("-------EGG WHILE LOOP---------\n") #DEBUG
            click(region1.getLastMatch()) # avoids another find() operation
            endWhileTime = time.time() #DEBUG
            checkLastMouseLocation(Env.getMouseLocation())
            endWhileTimeCheck = time.time() #DEBUG
            file.write(" while loop time --> %.2f \n" % (endWhileTime - startWhileTime))
            file.write(" after check position time --> %.2f \n" % (endWhileTimeCheck - startWhileTime))

        finalTime = time.time()
        file.write(" ***exit found egg time --> %.2f \n" % (finalTime - foundEggTime))
        file.write("-------EXITING FOUND EGG--------\n")
        file.write("--------------------------------\n")

Here is the results print to file.

-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 0.22
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.23
    after check position time --> 0.23
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 0.22
    ***exit found egg time --> 1.38
-------EXITING FOUND EGG--------
--------------------------------
FOUND EGG
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 0.22
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 0.22
    ***exit found egg time --> 0.77 <--EXPECTED run time
-------EXITING FOUND EGG--------
--------------------------------
============================!!!!!!!!ELSE i.e FAIL!!!!!!!============================checkRefresh
HUNT AGAIN
get RARE egg/nMouse last location
checkRefresh
FOUND EGG
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 3.23 <--- WHY IS THIS HAPPENING
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 3.22
-------EGG WHILE LOOP---------
Mouse last location
checkRefresh
    while loop time --> 0.22
    after check position time --> 3.22

 endWhileTime = time.time() #DEBUG
 checkLastMouseLocation(Env.getMouseLocation())
 endWhileTimeCheck = time.time() #DEBUG

... so the "mystery" happens in checkLastMouseLocation()
What are you doing there?

To get nearer to the problem, take care that you are using version 1.1.1

That function checks if the mouse has not moved. If it hasn't after so many times the program will refresh the browser. This is because sometimes the game doesn't show any eggs or other similar errors. here is the code.

def checkLastMouseLocation(currentMouseLocation):
    file.write("Mouse last location\n") #DEBUG
    global lastMouseLocation
    global sameLocationCounter

    #print("curr --> %s : last --> %s" % (currentMouseLocation, lastMouseLocation))
    if currentMouseLocation == lastMouseLocation:
        sameLocationCounter += 1

    else:
        lastMouseLocation = currentMouseLocation
        sameLocationCounter = 0

        checkLastMouseLocation()

and here is the refrseh code. Nothing fancy

#too many fails. Refresh the browser
def checkRefreh():
    file.write("checkRefresh\n") #DEBUG
    global notFoundCounter
    global sameLocationCounter
    global inActiveMode

    if ((notFoundCounter >= 30) or (sameLocationCounter >=20)):
        #popup("REFRESH!!!!") #DEBUG
        if region5.exists("1458036200954.png"):
            click(region5.getLastMatch())
            wait(4)
            hover(Location(0,0))
            wait(4)
            print("----PAGED REFRESHED----")
            #reset flags and counter
            notFoundCounter = 0
            sameLocationCounter = 0
            inActiveMode = False

Yes, it was a typo. and yes, the problem is in the checkLastMouseLocation() code. What I did was to comment out the function call and put a return statement in the function definition in case some other part of the code calls it. I then let the program run for about an hour and a half and the problem never showed up. It would usually show up after about 7 to 10 minutes. What I find odd is that this code is at least 2 years old and this problem never showed up before. So, why is it a problem now?!? Anyways, I'll change the code taking your advice into account. Thanks.

Thanks RaiMan, that solved my question.