Python timeit module execution confusion

I'm trying to use the timeit module in Python (EDIT: We are using Python 3) to decide between a couple of different code flows. In our code, we have a series of if-statements that test for the existence of a character code in a string, and if it's there replace it like this:

if "<substring>" in str_var:
    str_var = str_var.replace("<substring>", "<new_substring>")

We do this a number of times for different substrings. We're debating between that and using just the replace like this:

str_var = str_var.replace("<substring>", "<new_substring>")

We tried to use timeit to determine which one was faster. If the first code-block above is "stmt1" and the second is "stmt2", and our setup string looks like

str_var = '<string><substring><more_string>',

our timeit statements will look like this:

timeit.timeit(stmt=stmt1, setup=setup)

and

timeit.timeit(stmt=stmt2, setup=setup)

Now, running it just like that, on 2 of our laptops (same hardware, similar processing load) stmt1 (the statement with the if-statement) runs faster even after multiple runs (3-4 hundredths of a second vs. about a quarter of a second for stmt2).

However, if we define functions to do both things (including the setup creating the variable) like so:

def foo():
    str_var = '<string><substring><more_string>'
    if "<substring>" in str_var:
        str_var = str_var.replace("<substring>", "<new_substring>")

and

def foo2():
    str_var = '<string><substring><more_string>'
    str_var = str_var.replace("<substring>", "<new_substring>")

and run timeit like:

timeit.timeit("foo()", setup="from __main__ import foo")
timeit.timeit("foo2()", setup="from __main__ import foo2")

the statement without the if-statement (foo2) runs faster, contradicting the non-functioned results.

Are we missing something about how Timeit works? Or how Python handles a case like this?

edit here is our actual code:

>>> def foo():
    s = "hi 1 2 3"
    s = s.replace('1','5')

>>> def foo2():
    s = "hi 1 2 3"
    if '1' in s:
        s = s.replace('1','5')


>>> timeit.timeit(foo, "from __main__ import foo")
0.4094226634183542
>>> timeit.timeit(foo2, "from __main__ import foo2")
0.4815539780738618

vs this code:

>>> timeit.timeit("""s = s.replace("1","5")""", setup="s = 'hi 1 2 3'")
0.18738432400277816
>>> timeit.timeit("""if '1' in s: s = s.replace('1','5')""", setup="s = 'hi 1 2 3'")
0.02985000199987553