No connection to printer after reinstalling raspian

I dont know if I'm missing something but after I had to reinstall Raspian on my Raspberry Pi I cant't connect to my printer. I'll explain what I did because I have afeeling I missed something but first my set up:

Raspberry Pi B+ with Rasbian 4.4.21
Arduino 2560 Mega and a RAMPS 1.4
I'm running Pronterface on my PI with Marlin Firmware

Ok I isntalled the new OS with NOOBS, I did an update and an upgrade. I went to github and copied the dependencies from the readme-file. After that I installed Printrun (git clone [github]...). Then I installed the arduino IDE (sudo apt-get isntall arduino) and the Marlin Firmware (git clone [github]....)
I also installed some software vor myTouch Screen and qt5 for designing a GUI for the touch screen. But that shouldnt matter.

So is there anything I missed? Pronterface just tries to connect for ages (no warning or messages) and Arduino IDE says connection_timeout

EDIT 1: ----------------------------------------------------------------------------------------------------------------------------------------------------
Just after I wrote this I tried to uplaod a new firmware again and it worked (no idea why, i changed NOTHING).
Then i tried to connect with pronterface and it worked also. Although i did get an error:
"Attempted to write invalid text to console, which could be due to an invalid baudrate"
But everthing works perfectly. Still dont know about the baudrate. It is set to 115200 in both Marlin and Pronterface

EDIT 2:-----------------------------------------------------------------------------------------------------------------------------------------------
2 min after I posted the edit it stopped working. Pronterface wouldnt take any of my commands.
I reuplaoded the firmware again and this time Pronterface worked perfectly without the notice about the baudrate. I really dont know whats going on here

Edited 2 time(s). Last edit at 10/24/2016 06:29AM by MilloMille.

You are trying to flash marlin on the arduino mega or is it already flashed?

Marlin is already uploaded to the Arduino but I made some changes and reuploaded it again

Pronterface doesnt warn me about problems with the baudrate anymore but there still seems to be a problem with it.
When I try to print a G-Code my print gets randonly abortet. The Error I get looks like this:
Unknown Command: "2M105" (or "F300M105")
M105 is the command for checking the extruder temperature. It looks to me that two commands get mixed up. Like the second error could be the ending of a G1 command with Feedrate set to 300 but the temperature check gets put right behind it so the system doesnt recognize the command. This seems to be a Problem with the Baudrate but I don't know how to fix it. Pronterface and Marlin are both set to 115200. I think I will try setting it to 57600 and see if ill still have the same problems

Edited 3 time(s). Last edit at 10/25/2016 05:24AM by MilloMille.

Sorry guys I think I found the problem.
I use an active USB Hub for powering and connecting my Keyboard, Mouse, my Display and.... the Arduino.
It seems the connection from Raspberry to Arduino through the USB Hub is not fast enough. I still think its kinda wired because I ran the same setup for weeks before this, but ever since I connect the Arduino directly to the Raspberry I was able to print fine.
Sorry to bother you guys with my stupidity

Maybe the usb hub was underpowered or has a bad connection that drops to much voltage?