Hi, first off, fantastic program. I haven't found this issue described well aside from a couple of posts on the reddit r/krita forum.

I'm running Krita 4.0 through OSX on a 2012 MacBook Pro with a Wacom Intuos Pro M tablet.

When I summon the popup palette I will inevitably encounter a bug (sometimes on the first use, sometimes several uses down the line) in which the brush cursor freezes in place and will no longer respond to most stylus/tablet input. When this occurs I can't move the cursor, draw from the cursor, use the eraser nor summon the popup palette (via default first button stylus binding). This bug is easily replicated and will always occur immediately upon returning from the popup palette, it's just a matter of when.

I have CTRL-Z bound to the second stylus button and that will still work to undo previous work. I can also use the keyboard to CTRL-Z previous work. I can use the Wacom tablet radial menu to change the size of the brush cursor, but other than that I can only use the mouse/stylus cursor over the dock/toolbar/frame of the Krita window--nothing seems to work on the canvas aside from UNDO.

On the other hand, I've had luck using the program without the popup palette. I've had absolutely no canvas/brush freezing (yet) over extended use of the dock palette and dock brush navigator.

I also encounter the duplicate cursor bug (where the window resizing/vertical gridline cursor will appear until moving the stylus away from the tablet) that others have mentioned and I've also had a zoom cursor bug permanently duplicated on the brush cursor (until quitting and reloading the app) after using the trackpad to zoom and then returning to using the tablet. I did not select a zoom tool.

From my internet searches regarding this issue, I gather that the Wacom tablet drivers are finicky and that this could be the source of the problem. I checked the driver and updated and the OS is up to date as well. The issue still persists. Does anyone have an idea about what might be causing the issue?

I'm having the exact same problem. I'm running on an iMac using a Parblo A610 graphics tablet, so I don't think it's a problem with your tablet. I always have to restart Krita after this happens. Finding a solution to this bug would be great since the pop up pallet is extremely useful.