I dont know how to do configurations for persona 4. When I got it, I browsed through youtube for answers but none of the suggested solutions made me able to play "non-choppily" I hope someone here can help:

Intel Core i3 (1.3 Ghz)
Intel Graphics HD
2GB Ram
11"
Windows 7 Premium SP1
64-bit OS

No such magic, get a better PC.

I mean it works fine and there was a config on youtube that worked, only that it kept on flashing and it irritate my eyes...

get a real PC

1.3 is very too far to run it.

Post that config here.

Emotion Engine: Recompiler
IOP: Recompiler
EE/FPU ARO: Chop/Zero
Clamping Mode: None

microVU Recompiler for VU0&VU1
VU0/VU1 ARO: Chop/Zero
Clamping Mode: None

Frame Limiting Disabled
BFA:100%, SMA: 50%, TA:200%
Constant Frame SkippingL 5 to Draw, 6 to Skip

Speed Hack enabled:
EE Cyclerate:3 (max) /VU Cycle Stealing 3 (max)

Enable INTC Spin
Enable Wait Loop
Enable fast CDVD
mVU Flag Hack

Euro Console v.02
GS: GSdx 4600 msvc 15.00, ssse3
PAD: Lilipad svn r4510
SPU2: SPU2-X-r4660m
CDVD: Linuz Iso CDVD 0.9.0
USB: USBnull Driver

You mean you think it's "fine" with that setting? wow...

That settings are already over the line, and there's really nothing more you can do, except maybe trying new svn and turn down that frame draw/skipping to 2/2 and ee/vu hack to 1/2.