Mine does this too. Ever since i did my swap. For a while it was fine but it sux. Have a trick to open it by my self since my hood is fucked anyway. I open the door and pull the handle reaching through the door jam 0while i give the front of the hood a good kick. Ive messed with the latch so much movin it around and I cant figure it out. It really pisses me off too.

 

my friend reached in there and unhooked the cable, so we had to take out the middle bar thing to reattach it, there's my misalignment. and mike, the rubber things on the hood are adjustable just like the ones on the hatch, go check that ---- out next time you're under the hood.