In the EZ Flash IV Client try changing the save type to 1024kb SRAM (although it wont make the RTC work in Emerald). There is nothing you can do with the Pokemon Emerald rom's RTC due to how late it came out in the GBA life cycle. There is no RTC patch to this date either...it has been said that it isn't even possible.
My guess is you were using GBATA to do the patching but it has been said that GBATA has problems with the large Pokemon save files.