This has been explained before: THe register contents of the hardware-emulated Denise got lost, and the default values were applied when the config tool was launched. This caused the bug to appear with all ECS modes.
Even when using PAL ECS modes the black stripe on the left side does not appear. Now I have set PAL SuperHires Laced (ECS )and it works.
"re-installing" should really only be the last resort in finding such a bug. However, it's good to hear that it's resolved - I'd assume that one of the monitor types was at fault. Would have been nice to pinpoint the cause - did you make a backup before you re-installed the boot partition?
I also agree that "re-installing" should really only be the last resort in finding such a bug. In fact I performed the new installation on another partition keeping the old installation that still has the problem.