On the VTC, a red led indicate some timing is applied, either timing or turbo timing. Led will become green without it (0 timing, 0 turbo).
Same on the VX but a more solid one, pretty noticeable with the clear case.
On the VX, Led will be red with some timing added (either one) and blue without it.
My guess is you add some with the program card (or by updated it to V3).
Just plug the setup box, remove every bit of timing and you will have your blue led back (blinky mode).