I had this problem too. It seems like some of us have it and those that don't have no idea what, why, etc.
After upgrading to jd's knox-free 4.3 ROM, I decided to flash the dkp kernel. I did nandroid backups immediately before and after flashing the kernel... only a few minutes between them.
As expected, the filename for the first nandroid used a date/time from 1970 however the second nandroid had a correct date and time for both filename and "modified".
Since then, I have flashed CM11, restored back to 4.3, etc. which means the kernel has changed but my time and date are always correct in recovery.
I haven't restored any pre-dkp backups yet but when I do I'll update here whether or not the correct time/date stayed...