I own a Vexliar FL-20, not the FL-28 bit their principles of operation are the same. What kind of transducer do you have? The more narrow the cone, eg. 9° transducer, would possibly cause the issue you are having. Mine has a 12° transducer and don't have any issues...until deeper water of 30ft and deeper, where I have to turn the gain up quite alwaysto see my lure (the opposite problem you are having). This could be corrected by using a transducer with a more narrow cone such as 9°. What also will effect how your lure shows up is the type of lure you are using. Lures that sit in the water horizontally will show up larger than ones that hang vertically as there is more surface area on the lure to bounce back signals. If you have the dual beam transducer, try both beams to see if there is any difference between the two. Doesn't sound to me like there is a problem with your Vex. Lots of videos online from Vexlilar explaining the operation of their flashers and also some good ones on transducer operation, check them out!
Hope this helps you out a little bit!