Hi @dpog
"our board has two boot switches and a recovery-button" - I've seen this terminology before, the recovery-button was the reset button and a very misleading. iMXs don't have a 'momentary' press switch download ability.
"when it's pressed the board starts in download mode." Still sounds like it's in manufacturing mode (programming mode). iMXs don't have a momentary switch download ability, it's set by links or dip switches. If it is stuck in manufacturing mode then every time the recovery-button (reset button) is pressed it will reset and start programming mode again. You may find that you can do a download with UUU straight after power up without touching the 'recovery-button' at all, if you can, you're definitely still in manufacturing mode and need to trace those dip/link boot lines.
"When I manually change the mountpoint it boots completely." Correct, because if you're still in manufacturing mode and running UUU's uboot, pointing the mountpoint to eMMC post program will boot the board. Then on the next repower you'll be back to where you are.
The problem still remains that after I power the board down and up again, the SPL written by uuu is not loaded, hence no u-boot and so on. So I believe my problem might reside somewhere in the SPL
I seen this sort of thing a number of times particularly with custom boards, and no offense to the hardware guys but they might say it's nothing to do with mode links. Grab the circuit for the EVK and examine the connections around SW1101 and compare them to your custom board.
Also get your board's circuit out and trace the recovery-button and see if it just goes to the reset circuitry.
Hope you'll get to the bottom of this in time!
EDIT:
Go back to your evalkit (if this is an iMX EVK) and keep the dips in program/manufacturing mode at all times. Then see if you can duplicate everything you've mentioned i.e mountpoint to get it to boot after programming etc. If it's doing the same things as your custom board then it may help to prove what mode your boards in.. Also as it's the same chip and I imagine you've modelled your custom board off it, if the code works on the EVK it should work perfectly on the custom board proving your build.. It's doesn't matter if you're missing peripheral hardware as the drivers probe will fail and simply skip over. You should get to login.