try wiring back the VTM wire on the VTEC controller back to stock. so leave all the wires from the vtec controller how you have it connected but disconnect the VTM wire from the VTEC controller and rewire the VTM wire back how honda had it.

4-5 years ago i had APEXI VTEC controller and for some reason if the VTM wire is hooked up the car would not hit vtec.

try it and let us know