I didn't bother debugging the whole thing, just enough to find the first bug.
boolean isTS = (num1 != (num2 = num3)) || ((num1=num2) !=num3) || ((num1 = num3) != num2);
Using input 10, 20, 30:
(num1 != (num2 = num3))...translates to - Assign num3 to num2 and check that it's not equal to num1...so to use numbers it becomes
10 != 30 ---> which evaluates to true.
Now, because this evaluates to true I don't believe Java evaluates the ||'s since Java uses short-circuit evaluation. Thus, I believe your num1=num2 and num1=num3 have the same issue I just outlined.
Since you stated you're using Eclispe; Eclipse has a Debugger built in that can be a life saver once you know how to use it. I ran your code and watched when your varibles changed and found the above quite easily. In comparision it would have taken me much longer to find that bug if I tried to simply read the code and look for errors.