Rob, there are several possibilities and it sounds like you have a good idea what they could be but haven't had any luck yet.
For a comment (I assume that you are not displaying them) use the global edit function combined with the position ("center") to bring them all to the center of the components. Possibly make all comments visible with a global edit first.
A designator could be done similarly but then you have to re-arrange all your other designators afterward. Not so good but if you have to, you have to. Also make sure that all designators are visible with a global edit.
Another common one outside the board area is a polygon that was moved without knowing it, like when it was not deselected and you moved something else. This is doubly troubling when the polygon may have the remove dead copper turned on. If it is outside a valid net connection then the whole polygon disappears after pouring.
Is there any possibility it is a component primitive? Did you ever unlock component "primitives" (not the lock component)? That can be tough as well because you may not know which component it may belong to.
There are various selection problems with items outside your board or in the negative quadrant areas. Not all selection methods work, one that worked with one item may not work with another item.
You seem to have tried using the select outside area, I have typically not found it to work with your type of problem. Try this, use select all (S,A) move the board and all other items in a direction that should bring the errant item into view. Watch the bounding box around your selection as you move it to give you hints on which direction and how much to move. If you bring the item into positive quadrant space then you can easily deal with it.
If the previous methods don't prove useful try, select all (S,A), the use deselect inside (E, E, I) and draw a bounding box around your proper board area, be generous allow an inch or two at least around your board or other desired items. Once the proper board area is deselected then delete selected (Shift and Delete).
Hopefully one of those works. As a last resort you could try saving the file in ASCII format and edit it with some text editor to try and find the offending object. Edit it's coordinates to bring back to the positive quadrant at a known location.