I've just download avrdude 6.1 and run configure ; make . In config.log there was some complains to lusb0_usb.h file, but everything compiled correctly (without need to define uint32_t). I think you missing another devel library: libgcc-devel or something like that (so that can be reason, why #if .... not work properly for you). I can not tell You what package, because I am using different distro. Just look at config.log and check if HAVE_STDINT_H and HAVE_INTTYPES_H are defined as 1.
Just for case (maybe I am wrong, but i think there is problem), could you please create test.c file (for example in /tmp/ ) with following code:
#include <stdint.h>
#include <inttypes.h>
int main(void)
{
uint32_t i=-1;
i++;
return i;}
Then type "gcc -Wall test.c". It should not produce ANY warning. If does, please post it here.