New here, hello!

[ssakash]

try dev build and gsdx 9 hardware mode .

Why ? Dx11 is better overall.

[Guardian of Harmony]

That's because, you haven't updated to the latest pcsx2 version. Update to the latest version of pcsx2 to get better compatibility and support on the forums.

Okay I updated to the latest version from the site and Sora's leg was missing again but returned to normal upon entering the first area, so I'm gonna play through Traverse Town unless there's a problem and report back to ya. Thanks for helping man!

[Brock lessner]

Why ? Dx11 is better overall.

dx11 is better , it just to try if gsdx 9 can fix it or not ?

[Ryudo]

D3D11 runs fine in this game. No reason to run D3D9.

Again, there shouldn't be any issues with graphics in the latest releases. (Even the stable 1.2.1).
We still don't know what his settings are either. If he changed something in speedhacks or hardware hacks that could easily bug the game.

[Guardian of Harmony]

Why ? Dx11 is better overall.

So I froze on entering the Second District. Any ideas?

[Ryudo]

Post your PCSX2 settings, all of them.

[ssakash]

It's probably because of enabling speedhacks, use the default settings.

[Guardian of Harmony]

Post your PCSX2 settings, all of them.

Everything is at the default settings When I got it except for the clamping modes on VU and EE/IOP. No speedhacks were used either.
Picture of current plugins. http://gyazo.com/6aa134d838e71df751859d30f164c462

[Guardian of Harmony]

It's probably because of enabling speedhacks, use the default settings.

Everything is at default settings and no speedhacks were used.

[ssakash]

Try loading your save from memory card rather than loading from savestates and check whether the problem persists.