I am having issues with my keyboard hen using graphical tools like inkscape or gimp. However I every now and then after working with them I cant use my keyboard. I have to press the key several times to type a letter.
I used to get a KDE dialog suggesting using some mode I cant remember which happens after holding the Ctrl key pressed for a while. I wonder if somehow that mode is being activated while working with these tools, and if I can get a way to diable this.

Sounds like you have "Slow keys" enabled somehow. Open System Settings > Accessibility > Accessibility > Keyboard Filters, and make sure both "Use slow keys" and "Use bounce keys" are disabled.

As these features are both underpinned by X itself, it is possible that Inkscape/GIMP are somehow accidentally activating them, so toggling the setting may return your keyboard to it's normal setting.