Hummm. I just tried this
In[1]:= var = Input["Please Enter an Integer"];
Sqr = var^2
Out[2]= 121
Maybe try starting Mathematica fresh, just type exactly your two lines of code, hit shift and enter, tap the 1 key twice to see 11 in the input box and click the OK button. Don't do anything else, no extra mouse clicks, no executing a bunch of stuff first and report what happens.