Some tablet drivers allow (and even require) to create profiles for different applications. For example maybe you want to have different button mappings or shortcuts for different applications. The Wacom configuration manager allows this too.
Btw the Problem you are facing is not exklusive to Krita, it happens in Photoshop too.
Perhaps you have to disable/enable windows Ink in the tablet settings too, as shown in the blog I linked. It needs to match the setting in Krita.