Depending on how you did your hack, the TV may no longer be able to handle interlaced inputs properly. If you attempt to display an interlaced input as though it were progressive, it will appear VERY flickery, especially with lots of hard lines as are common in computer graphics. How are you inputting sync to the TV?
Even if it is able to handle interlaced signals properly, it'll always appear flickery, as ahofle indicated, especially again on computer graphics. This is just the nature of interlaced inputs. If the TV happens to support 480p, you could run it at that resolution (which is "VGA"), but I don't know that any of the Trinitron TV sets supported this.