connected DIN MIDI Out cable disturbs encoder

The internal Pull-Up resistors habe about 50kΩ, so they are very weak. 
The lines can easily receive radio signals.

You need stronger Pull-Up resistors, for example 2,2kΩ. Also your 
capacitors are on the wrong side. The encoder contacts will shorten the 
capacitors, which leads to short pulses of very high current.

Better:

1

        2.2kΩ

2

3

3,3V o--[===]--+    100Ω

4

               |   

5

µC o-----------+---[===]---o Encoder contact

6

               |

7

              === 

8

               |

9

GND o----------+-----------o

i just figured it i make the ground connection closer to the power 
supply the problems disappears. any idea what could be happening there?

Search for en explanation of "ground loop" and why GND connections shall 
form a star to work properly. The web is full of related documentation.

Hey Stefanus!

Thanks a lot. your circuit seems to work much better - meaning without 
any problems! i placed some pullup resistors, and you are right: the 
capacitors should be placed behing the 100 Ohm resistors.

im still working on a breadboard to test out all the components. so 
there is not really any propper GND layout yet. but it will follow your 
advices when i create the pcb layout.

The main related pyhsical effect is:

Every line has an inductance and a capacitance. So every line is more or 
less an antenna (more for higher frequencies) which sends and receives 
radio signals.

Also the purpose of GND is a unique common potential that all signals 
are derived from. If you have a few centimeters of GND wire, it will 
have already more than 0 Ohm. As higher the frequency, as higher the 
resistance. And resistance together with currency produces a voltage 
drop.

So GND is not the same GND everywhere, and that arises lots of different 
problems.

> im still working on a breadboard

Breadboard make it even worse because the usually have contacts and 
cables made from iron which has a significantly higher resistance than 
copper.

Consider to solder the power supply wires and plug only the signal wires 
which are less critical.