Melzi 2.0 with Marlin 1.1.9 endstops are not working (4 replies)

Hello there!

I have a Trony P802 which was working fine with the factory shipped Reprap 0.91 and with Marlin 1.1.9 which was compiled and uploaded by me.
Both versions worked fine, until I made some changes in the source files, recompiled it and unfortunately I uploaded the wrong binary without the bootloader.
After that, I successfully reuploaded the working binary with the bootloader, but the endstops - at least on the y axis - has stopped working, autohome fails and the servo motor just tries to move the heatbed after it reached the top end.
I found that part on the wiki page: X axis only moves in one direction and/or Endstops do not work.
I have the latest Sanguino version (1.0.3) in the Arduino builder files, so the fuse settings had to be correct from the beginning, right? I'm asking, because after I reuploaded the binary, I had to also change the fuse setting with avrdude, because - maybe - all of them were FF. But this didn't had any effect at all.
I'm afraid for some reason the controller doesn't applies the written changes, can the bootloader overwrites it?
I also had a try with the full working Reprap dump (created with avrdude), but no luck.
I also had couple of other ideas, like uploading the bootloader with ISP and upload the whole firmware on USB an so on...

[user@comp]: /media/ramdisk>$ sudo avrdude -c usbasp -p m1284p 
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.02s
avrdude: Device signature = 0x1e9705 (probably m1284p)
avrdude: safemode: Fuses OK (E:FD, H:DE, L:FF)
avrdude done.  Thank you.

Thanks