The problem is Mac-only. It has been introduced some time AFTER Tcl/Tk 8.6.1. The below replication steps do not cause flickering there.
Replicated with latest source (8.6.3) as of 2014-12-21:

Do:
- Run the below script in Wish.
- Move the mouse around in the window.
- Also try resizing the window.

Happens:
Each time the mouse motion even triggers, the since-long destroyed scrollbar keeps appearing (flickering) on the screen.

Expected:
That the scrollbar is simply gone, since it was destroyed.

Here's the script:
###########################
proc main {} {
	console show
	wm geometry . 800x600
	frame .f -width 750 -height 550 -bg grey75
	place .f -x 50 -y 50 -anchor nw
	button .f.b -text hello
	place .f.b -x 100 -y 100 -anchor nw
	set w [create_window .f 10 10 300 300]
	update
	destroy $w

	bind all <Motion> {
		.f.b configure -text [clock seconds]
	}
}

proc create_window {parent_w x y width height} {
	set w $parent_w.c_container
	frame $w -bg grey75 -bd 0 -width $width -height $width
	scrollbar $w.vscroll -command "$w.c yview"
	canvas $w.c -highlightthickness 0 -width [expr {$width - 15}] -height [expr {$width}] -relief sunken -bg grey85 -bd 0 -yscrollcommand "$w.vscroll set"
	grid $w.c -padx 1 -pady 1 -row 0 -column 0 -rowspan 1 -columnspan 1 -sticky news
	grid $w.vscroll -padx 1 -pady 1 -row 0 -column 1 -rowspan 1 -columnspan 1 -sticky news

	place $w -x $x -y $y -anchor nw
	return $w
}

after 10 main