Boolean and Integer are strings after serialization
update_post_meta uses update_metadata you can find it's code here in that function if you have a look at line 119 you will see that the meta_value is passed to wp_unslash which return value is a string (the function that changes the data type is stripslashes_deep)
As a workaround you can serialize the value before passing it to update_post_meta()
EDIT:
Found the issue: before 3.6.0 update_metadata had on line 117 this code:
$meta_key = stripslashes($meta_key)stripslashes is a php function that returns a string.
as of 3.6.0 that line looks like:
$meta_key = wp_unslash($meta_key);which stripslashes only string type meta_keys.
An update to wordpress 3.6.0 or above will fix the issue.