I am facing the same issue with perl 5.18.2. Basically miniperl creates files with modification date in the past (some 59 seconds), while the Makefile.PL had good modification date (i.e. according to system clock).

Since the filesystem was located on a Network Attached Storage, I simply moved the source directory of perl to some other storage and it solved the problem.

(miniperl used to be on the NAS, while make was on an internal hdd. But I still don't understand why the modification dates were affected.)