Emulator

I couldn't reproduce the warning since its random and it think you have to play for a while to get the warning. Here is the GCI save. play file 2 and see if you get the message. As for the dump information i dont know where its at.
http://www.mediafire.com/download/vb3dkn196fzc16i/G8ME_mariost_save_file.gci

here are my settings and the rest of the settings are default
http://imageshack.com/scaled/large/716/38kd.png
http://imageshack.com/scaled/large/836/r3xi.png
http://imageshack.com/scaled/large/41/xpvh.png
http://imageshack.com/scaled/large/404/yu5g.png
Game Id:G8ME01

D3D11 is the worst back-end for Paper Mario: The Thousand Year Door. I don't think it'll fix your crash (I don't think it possibly could cause it) but it'll stop some flickering issues that crop up every once in a while. Otherwise, your settings look fine.

I didnt use any cheats

Did you check your MD5 hash?

Where do i find the MD5 hash?

If there is no reply soon, I will assume invalid and mark the issue as such.

Regardless, find you disc MD5 by loading it into a program called "winmd5free"

Give us the output of that and we can verify whether it's a good dump or not on redump.org.

It seems to be fixed. Haven't had any warning since, and im almost done with the game.

I'm not sure if it's related, but me and a user on TASVideos reported Dolphin crashing as soon as a savefile within the punis was loaded:
http://tasvideos.org/forum/viewtopic.php?p=363588#363588

The save file in question is here:
https://www.mediafire.com/?9wy8qadwv5tcf5d

I have a savefile in the same area and it works fine. I'm really thinking someone is doing something is wrong.

Well, I just tested it on the builds without the fix, namely the one in the download page, 4.0.2, and it seems to be able to load the savefile without problem. Yet when I tried it on dolphin-master-4.0-604-x86.7z, it crashed.

What fix?

er...since I can't seem to edit my comment, the "fix" I mentioned is the one referenced in the forum thread.

If it helps, the build that the savefile crashed on is
https://dolphin-emu.org/download/dev/45f74840d6a32f278fedbe0381e7db1127669ce5/

Ok, and update:
I tested loading the savefile
https://www.mediafire.com/?9wy8qadwv5tcf5d
on the latest build:
https://dolphin-emu.org/download/dev/5fb8d07953a808b71e6cae6c2e6ed6bd8e104364/

and it gives me this:
http://imgur.com/nLz2Hfb

I'm using OpenGL, if that helps.

This seems to only affect Win32 builds.

Is everyone who is crashing using a Win32 version of Dolphin?

If so, I may have a fix in hand. It's a weird compiler optimization bug, and the fix is no less weird.

Here's a Win32 custom built version without the crash. Please test and send feedback:

https://dl.dropboxusercontent.com/u/15465721/Dolphin.zip

I just checked the build you provided. It doesn't crash Dolphin now, but the puni graphics have become glitched once more:

http://i.imgur.com/IQvD7We.png

Ok, I can confirm this has nothing to do with the graphic bug, since for revisions as far back as this:
https://dolphin-emu.org/download/dev/94f8c68a35b6b29e6670092ebc78e0dcd206463e/

Seems to crash dolphin upon loading the savefile. :o

The graphical bug is its own issue and well known. This issue is for the crash/warning stuff.

The next big bbox revision (it's a slow work in progress) will fix this and the puni graphics as well.

Looking forward to seeing it :)