Mega 1280 only working when set as ADK 2560

So, I got a Seeeduino Mega from Seeedstudio. I have it in and for some reason, whenever I try to upload a sketch to it with the board set to "Arduino Mega 1280" (the two boards are equivalent save the extra pins on the Seeed variant), I get either an stk500_rcv() error or a timeout error. So I saw this guys post (http://www.seeedstudio.com/forum/viewtopic.php?f=16&t=3869) on how he fixed his and it involved setting up the seeeduino board as a 2560 and then sending your code. Oddly enough, I have simply changed the board type in the arduino IDE to Mega ADK/2560 and it works fine.

So, I imagine this isn't okay, and I need to be working with the ports, which are hardware specific. The serial commands work fine, but I cant use this as a 2560.

I am running Linux 12.04 Arduino IDE 1.0.

If it helps, I can include my boards.txt

Also, the loopback test works fine (don't know is this is relevant or not). Just throwing it out there

Don't 1280 & 2560 have the same features, but just less memory in the 1280?

Could try updating to 1.0.2, see if that helps.

Thats what I thought, but I am going to need to be able access the ports directly (Arduino Reference - Arduino Reference), and I believe that the 1280 and the 2560 have different ports (not sure, just assuming). Going to try testing on a Mac today at school.

Why would the change in memory affect the ports?
640/1280/2560 all have the same ports

ATMega2560 Summary.pdf (1.01 MB)

Well i'll be damned. Sorry, I was a bit intimidated by the huge PDF xD. Also, for anyone in the future who might see this post, it didn't work on mac or pc. Very peculiar.

The NEW Seeeduino Mega's ARE 2560's. Are you certain that you have the older 1280 version?

Ohhhh, well, thats a very welcome surprise xD. I will contact the seed guys so they update their tutorials =)