Not sure if related to pointer interlace or not but that sounds like the issue or the affect that is happening. On a hires screen (no interlace), why would the pointer need to laced? I can kind of understand it for hires interlace but not hires.
The "http://aminet.net/package/util/misc/LacePointer" only works for lores pointer mode. LoRes pointer mode does not seem to have any strange affects in the aspect ratio from what I recall or seen recently in other screenmodes...I haven't check thoroughly though.
I was just stating that the pointer on a Hires PAL or NTSC screen will not be interlaced even if in an interlaced mode. I suppose Commodore chose this behaviour because an interlaced pointer would drive the user crazy without a flicker fixer (only minority of users had these)...who knows?! That's my best guess.
Interestingly though, when this happens and the user is using a Hires pointer on a Hires Laced screen, obviously the pointer accuracy is only at half vertical resolution because it's not laced...but this isn't quite true. I just tested it with the multiple selection (hold left mouse down to select icons) and you do get the full vertical resolution accuracy in reality, but the pointer only updates it's vertical position on every 2nd row (it can't do any other as it's not laced). If you use the keyboard controls to move the mouse you can clearly see this behaviour - a movement left or right is one keypress at a time per pixel, but for the vertical direction it takes two keypresses to move the mouse pointer that you see, but Workbench does 'see' that bit inbetween that it couldn't show with the pointer so the mouse does actually run at full laced resolution. I think there should be an option to lace the pointer in interlaced screenmodes via Pointer Prefs. I haven't tested A multiscan interlaced screen, but I'd bet that the pointer would not be laced either.
