Closed loop - encoder/position not updating while moving

backyardengineer wrote:

It has somehow to do with the enabled stepper motors. As soon as the drive gets the enable signal the pins don´t change anymore (viewed them in hal config). Wen i check with the multimeter, the signal seems to be switching between 0.2V an 24V correctly (both with stepper enabled/disabled). Maybe it is an issue with those cheap breakout boards ?

That is almost always an interference/wiring/grounding/shielding issue, and cheap BOB's with optocouplers are very slow so will limit speed a lot, the ones with input buffers should be OK.
But, 24V? What encoders are those?
Upload some pictures of the wiring here so we can have a look.

Some clarifications before this goes sideways:
-COM0/COM1/COM2 are referred to serial ports, be it RS232 o other, usually.
-LPT0/LPT1/LPT2 and sometimes only P0/P1/P2 are referred to parallel ports, usually.
What are you referring to with COMn ?
Serial ports are pretty much useless with LinuxCNC, except for some stuff.
Parallel ports, also known as IEEE 1284, are used for machine control still, are perfectly usable with LinuxCNC, but have limited pulse rate capabilities compared to Mesa board.
Reasonable pulse rate or encoder pulse rate for parallel port would be 10000-20000 PPS, sometimes can go to 50000 PPS with a bit of luck/tweaking the BIOS.
At 3000 RPM, that is 50 RPS, so for a 100PPR encoder ends up 5000 PPS, and for a 1000PPR encoder it is already way to fast for most PC setups, see above.
Now convert that to mm/m, as you gave us no info about drive/gear/reduction.
After all that, yes, you can use a parallel port, yes it will work with encoders (2 max normally per port), and yes, you can lower the speed if you have higher count encoders.
But first, fix the wiring and get rid of interference/bad grounding.