It seems that 03 is after 04. Is this the case?
Also it seems that the file is written successfully:
stat("/home/mer/.config/codeblocks/default.conf", {st_mode=S_IFREG|0664, st_size=36236, ...}) = 0
lstat("/home/mer/.config/codeblocks/default.conf", {st_mode=S_IFREG|0664, st_size=36236, ...}) = 0
access("/home/mer/.config/codeblocks/default.conf", W_OK) = 0
lstat("/home/mer/.config/codeblocks/default.conf", {st_mode=S_IFREG|0664, st_size=36236, ...}) = 0
open("/home/mer/.config/codeblocks/default.conf.temp", O_WRONLY|O_CREAT|O_TRUNC, 0100664) = 5
write(5, "<?xml version=\"1.0\" encoding=\"UT"..., 47512) = 47512
close(5) = 0
rename("/home/mer/.config/codeblocks/default.conf.temp", "/home/mer/.config/codeblocks/default.conf") = 0
Do you have dropbox or something similar setup for your home folder? I've heard complaints of brokenness in such setups.
Does the modification time of the file changes?