hmm...I think my tranny does the same thing too. It rarely happens but when it does, it scares the crap out of me. It's like I'm in first gear and I floor it then it hits the rev limiter hard and the car bucks/jerks uncomfortably, bounces back a couple RPMS and kind of waits a second or two to upshift? Is this what you're talking about? Because I think I've seen a thread about it. I don't think its because you have mods...cause my car does it and I'm bone stock.
Not sure about your tranny though cause I have an auto SE-R. My car usually shifts nicely and when I'm easy on it. But sometimes it shifts hard. I havent experienced that 1st to 2nd gear jerk lately, but I guess its always good to inquire about it to the the dealership or change your ATF.
2k3 Blackout SE-R (auto)
Mods: imported cross from Italy hanging from rear view mirror