I have seen this problem asked in the forum by another user but no solution given. I have a big problem with the brush tool, and clone as well, being offset from where I am trying to select. As mentioned in a previous unanswered post; "there is a shift of the pointer position before and after the mouse click. If I select a brush for example, as soon as I click, the pointer shifts towards the bottom right of my screen, and then a straight line connecting the pointer position before and after click is automatically drawn. This shift is larger and larger when the pointer position goes from the top left towards the bottom right of the screen. It is of the order of a few centimeters. Most of the photopaint tools are unusable. " I am having the same problem and the tools are unusable. My updates are current (PP 6.4) in Windows 8.1 on an HP i7 computer. I have re-installed the program and re-set the workspace with no improvement. HELP!
Have you reset all brush types yet?
What kind of mouse are you using?
First thing I would check would be my mouse settings. There was an issue a "Snap to" feature with Microsoft Intellitype which would make the mouse pointer behave erratically like you mentioned. If you have something other than a Microsoft mouse (e.g. different brand mouse, pen tablet, touchpad, touch screen, etc.) check its settings to see if there is something that might cause the mouse jump around the screen).
Try UNchecking (one at a time) the Enhance pointer precision or Snap to on the Pointer options tab of the mouse settings.
Microsoft has a Mouse and Keyboard Center you can access in Control Panel. You can check settings there, change settings specific to a program or "return to default."
Other than that, perhaps it's related to the new on-the-fly transparency feature added with the X6.3 update. This feature lets you interactively change the transparency of the brush tools by holding down the ALT key.
May not be related...Holding down ALT+SHIFT lets you start a brushstroke in one place and draws a straight line when you click again on the screen. Sort of like it's shooting the stroke from the pointer.
That's my best guesstimate, FWIW.