Turn off OpenGL and see if it makes a difference, likewise, check your settings for the cached tiles and use less levels perhaps...
I just tried to reproduce the problem in Ps CS6 and can't. For me the Pencil Tool draws single pixels right where the cursor is shown.
Did you try the things Mylenium suggested?
Mac or PC? What video card do you have?
I did the same tyhing with the same results, except that at full zoom a single pixel might be slightly offset from the cursor. I was not able to reproduce the situation though.
Other possibly relevant situations that I can remember, are items moving slightly when placed. I also found this
And this one in which Chris Cox suggests the video driver.
Do we know what system Queets is using? platform and OS version?
Also, do make sure that you did not scale your operating system interface, or change the operating system cursor size.