Problem:

The problem comes from using the second argument of dynamic. When the user modifies the variable, the second argument will be used. However, the autorun does not use this second argument.

Note the difference in the path of the locator when the user moves it, and in the autorun:

Manipulate[SliderPane[Dynamic[pt,(pt={First[#],-First[#]})&],Graphics[Circle[]]],{{pt,{0,0}},{-1,-1},{1,1},ControlType->None}]

Think what a large problem this becomes when the locator is supposed to follow a curve:

Module[{func=Cos[x],var=x},Manipulate[SliderPane[Dynamic[pt,(pt={First[#],func/.{var->First[#]}})&],Graphics[Circle[],PlotRange->{{-2π,2π},{-1.2,1.2}}]],{{pt,{0,1}},{-2π,-1},{2π,1},ControlType->None}]]

Workaround:

Here's the workaround for the specific problem above:

Manipulate[pt={#,-#}&[autorunvar];SliderPane[Dynamic[pt,(pt={First[#],-First[#]};autorunvar=First[pt])&],Graphics[Circle[]]],{{pt,{0,0}},ControlType->None},{{autorunvar,0},-1,1,ControlType->None},AutorunSequencing->2]

Here's the workaround for the locator that follows any function:

Module[{func=Cos[x],var=x},Manipulate[pt={#,func/.{var->#}}&[autorunvar];SliderPane[Dynamic[pt,(pt={First[#],func/.{var->First[#]}};autorunvar=First[pt])&],Graphics[Circle[],PlotRange->{{-2π,2π},{-1.2,1.2}}]],{{pt,{0,1}},ControlType->None},{{autorunvar,0},-2π,2π,0.05,ControlType->None},AutorunSequencing->2]]

Instructions:

Seperate parameter 'autorunvar'

'autorunvar' is unavaliable to the user

AutorunSequencing -> placement of 'autorunvar'

'autorunvar' influences locator point in manipulate body

locator point influences 'autorunvar' in dynamic in manipulate body or in dynamic in manipulate variable declaration