I thought I would add some experience with this issue that may be of help.
I have a large SAN RAID unit at work, using 15x Seagate ST3750640NS drives (Barracuda ES, 750GB, SATA300, NCQ, 16M cache). The firmware on these drives is not the same as the desktop models, but is labeled similarly. While the desktop versions have 3.AAE or 3.AAK firmware (or other versions), my Barracuda ES drives have 3.AEE or 3.AEG firmware. Note the "E" in the middle character vice the "A", this probably notes the difference between the desktop drives and the ES drives.
Anyway, I had a drive fail in my SAN last week, purchased another ST3750640NS to replace it, and it had 3.AEK firmware. As soon as the array was running on that drive, it showed a marked drop in performance. Now, this doesn't necessarily indicate an inherent problem with the 3.AEK firmware, but rather that the mismatch between the other 14 drives (on 3.AEE and 3.AEG) and the single 3.AEK drive was causing a problem.
I called Seagate and ended up doing two things to resolve the issue, but found out a few things that are very interesting. First, the 3.AEK drive is not only different firmware, it's different hardware. Apparently, the controller board on that drive is a different, newer revision. This is evident in the internal Seagate part number. Drives with 3.AEE or 3.AEG firmware have a part number of 9BL148-301, while the drive with the 3.AEK firmware has a part number of 9BL148-303. Seagate told me that because the controller board is different, there is no way to flash the firmware to a matching version because no other firmware other than 3.AEK will run on that controller board.
They offered to RMA the drive for me and give me a -301 drive with 3.AEE firmware so that it would match the rest of the drives in my SAN.
They also gave me a password-protected web site where they have firmware flashers. The site was password-protected with a key that was tied to my technical support case number, and is only open for my password for 9 days. It also restricts me to downloading only the flasher specific for my drive model, and my requested firmware. He gave me the 3.AEG flasher, which I will use soon to flash all the 3.AEE drives in my array to 3.AEG, thus they will all match. He said that 3.AEG is the latest firmware for the -301 part.
Even though all of this is in the context of Barracuda ES drives, I suspect that the overall issue is identical for the desktop drives using AAE and AAK firmware. i.e. The hardware is different, and flashers for the drives do exist but can't change AAK drives to AAE drives because of the different controller board.