I am using a Mega2560 with an Ethernet shield and RTC. I set the time on the RTC and the library functions work properly. However, when I create a files on the SD card, they always have the same creation date/time of Sat 01 Jan 2000 01:00 AM PST.
The SD card doesn't automatically know you have a RTC connected so it can't grab the time from there. Have a look at the functions available in your SD library. It may be possible to set the create date in a separate function after creating the file.
You might find it useful to use the date as a filename. I just change the date at midnight but you might want several and I'm sure you could add the time as well.