I just noticed that re-bundling in EC2 instance is not working. Google told me that it is due to the incompatibility between latest rsync and relatively old kernel used by EC2 (2.6.16).

In the thread about this issue, 5 possible workarounds are presented. However, none of them are easy under gentoo without messing up with ebuild/emerge. I found another way, and you don’t need to regenerate the configure file for rsync at all, all you need is to comment the following line in the config.h file (which is generated after you run the configure script):

#define HAVE_LUTIMES 1

then make and make install, all should be fine now.