Not sure why, but I discovered that the optical sensor was wiping out my eeprom every time I powered up my APM 2.6. I had to erase my eeprom and reprogram the APM every time it happened. I'm just going to remove it rather than troubleshoot it as the position hold with the GPS is great by itself. Just wanted to give folks a heads-up in case they were experiencing the same thing.
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So, after writing the reply a new version of ArduCopter (3.1) came out so I checked the changes and there was a fix to it. So it was a problem of the ArduCopter software.
Well, I figured it out after the whole day testing why I couldn't connect to my APM. I just found it when I was searching the solution. Is anyone there who found the solution? I would like to use my quadcopter also inside the buildings so I need the sensor to be working. But it corrupts the EEPROM even if there is no optical sensor connected and I just turn it on. So, it is possible to be also another problem but unfortunately I don't know it now.