meelis
I changed phpbasedirectory primary ibay ....
I suggest you undo that change and then see if things work OK again.
If so, you can then work out how to correctly make the required change.
You may want/need to move your Primary ibay content to a regular ibay, so that way if you make any changes to the ibay folder it will not upset the rest of your server's main domain functionality.
Just a guess & a suggestion, as I did not research your problem.