I had the same problem, and it turned out to be my reset line.  You cpuld try a 10kbigger resistor, and a 22pf cap on a breadboard.  The mkii pulls the reset to gnd at the beginning,  and if it can't you'll get the error

Silly me, i hooked up tx->tx and rx->rx. Thats probably why im having trouble.   I'll try to switch them today.   It kept timing out when i tried to upload. Guess that would be why.  Thanks guys!

Can I use the ftdi232 with a mega2560 wiring it up just like its on a uno?  I noticed the baud rate changes to 115200, but is this just for the micro itself, or does it effect the ftdi chip?  Anyone ever done this? 

Problem Solved!  Thought I'd let everyone know just in case they are having a similar problem. It was the reset line.  I made one on a breadboard going from 5v to a 10k resistter.  the resistor goes to the reset switch + side.  The other side straight to gnd.  right after the 10k resistor, I put a 22pf cap.  Everything works perfect.  Bootloader uploaded fine.

Thanks everyone that helped.

Yeah thats exactly what i tried.  It wouldn't get past the beginning of the program where it pulls the reset line low, and checks for clk.

I put my multi meter on reset and ground right at the pin.   It went to about. 02v. I did it with a known good board and ot went down to .005v. Do you think yhis is enough to cause the issue?

I see what you mean the programmer controls the line.  I tried using the uno as an isp, and coudnt get it to work either.   It works on a known good 2560, but not my board.  I just do not understand why it wored until i tried to bootload it and now nothing. 

I guess i will order another chip and try again.

Any other ideas?

Ok im finally getting somewhere.   I got the bootlader on one of my boards.  Looks like its the reset line causing the problem.  I started desoldering pieces of the board, as soon as i took off the resistor on the reset line the bootlader loaded with no problems.

How exactly does the reset line work?

Its the stk500v2 bootloader.  Make sure it's v2 this version supports the higher memory adresses.  The hex file is already in the arduino IDE.  I forget where, but im sure you can google that.

Just tried it on another pc, and i get the same error.  I figure this means it has to be the board or the firmware on the programmer.

I tried to upload new firmware in atmel studios 6 i first uninstalled libusb driver and used the jungo driver.  It still can't find the programmer even after jumping the two pins on the programmer.

Do you guys know how to update the firmware?

If i can get studio 6 to communicate with it i'll try to program in that.

Once again, thanks for the help guys!

Just jump the rx and tx pin? How do i send the data in the arduino ide gets hung up on upload.  I think it is looking for a handshake from the software.   I think it will timeout, i haven't left it that long.

haha yeah I'm on a pc.  All that shows up on my ports is lpt1.  No com ports anywhere.

I should also say I just got my ftdi chips finished on the board and pluged them in.  The computer saw them and makes the noise when i plug them in and unplug them.  Maybe this did something to screwy to my com port settings.

I have a micro usb going to the ftdi and a lm358n opamp to power the board.  Power is working fine.  I dont know about the ftdi since i dont have the bootloader on it to test it out.

Any other ideas?

I thoght the same, but I am using the good driver libusb.  I even tried reinstalling it.  It seems avrdude can not find the mkii on any port its trying to use the stk500v2 instead.  When I type in the port in avrdude it cant find anything. I tried com0 - com9.  No com ports show up in my device manager.

How can I tell what com port the programmer is on?

Yes powered it up three different ways.  avrdude shows it sees good target voltage.  Reset pin has a 1k resistor, and both lights are green on the programmer.  in avrdude it shows avrdude: stk500v2_command(): command failed  and a couple other things about stk500v2. 

I press shift and click on the program button in arduino IDE, data goes to mkii, first light flashes green like data is moving, second light quickly flashes red, then I get the error.

This all started right after I tried to burn the stk500v2 bootloader.  It did something for about 10 sec then I got an error.  I didnt right it down though 

Do you think its trying to use the bootloader instead of the mkii.

Oh, and I tried the clock thing with no luck.  avrdude shows sck period    :8.00us
I do have the external 16mhz crystal already hooked up.

The programmer doesnt show up on a com port all I see is the lib driver and it is under that.

I'm going crazy!

Yeah i have read that already,  but thanks.  Today im going to try and use a known good clk source, and the rest hooked up to the new board.  Hopefully its just my clk fuses.

I built a tiny 2560 with a ftdi chip and a 16mhz crystal.  I had it working with my avrisp mkii using the arduino ide without a bootloader.  When i uploaded the blink sketch it seemed it was running at a 1 mhz clock speed.  I decided to burn the bootloader to hopefully set the right speed,  and allow me to program through my micro usb port.

I selected the board,  then selected my programmer, and clicked burn bootloader.  It came up with an error, and now i cant even upload like i was before.

The lights are both green on the avrisp.

I had an uno, and a mega that i was able to burn the bootloader on.   I know my circuits are ok because it worked before.  

It seems like it isnt looking at the right com port or something.  

I even tried it in avrdude and ot says it cannot find the port file

Any help would be greatly appreciated!  Thanks in advance.

The only thing that is different is the clk speed on the new boards. I believe they are still using the internal oscillator at 8mhz.