Emulator

Game Name?
Games tested where the problem occurs (I compressed these games and did NOT eliminate the first partition):
Sonic Colors - SNCE8P
NiGHTS: Journey of Dreams - R7EE8P
Kirby Epic Yarn - RK5E01
Sonic Unleashed - RSVE8P
Resident Evil 1 (Archives) - RE4E08
Sonic & the Secret Rings - RSRE8P
Sonic & the Black Knight - RENE8P
Sonic Riders Zero Gravity - RS9E8P
Super Mario Galaxy - RMGE01
Mario Kart Wii - RMCE01
Sonic & Sega All-Stars Racing - R3RE8P
Pikmin 1 for Wii- R9IE01

Games tested where the problem DOES NOT occur (I compressed these games and removed the first partition, leaving just the partition with the game data):
Xenoblade Chronicles - SX4E01
The Last Story - SLSEXJ
Pandora's Tower - SX3EXJ

Game ID?
see the list of games above for their IDs

What's the problem? Describe what went wrong in few words.
When attempting to extract the .DOL from Wii games that consist of multiple partitions (ie - every Wii game that hasn't been scrubbed after they have been dumped), the .DOL file that gets created is only 1kb in size. Games that have been scrubbed (which usually eliminates the first partition containing IOS files) output the .DOL file correctly when extracted.

What did you expect to happen instead?
The .DOL file is supposed to be correctly extracted from the partition containing the game's data.

What steps will reproduce the problem?

1. Take any Wii game disc image (compressed/uncompressed) that hasn't been scrubbed and have the game appear in Dolphin's game listing in the main window.
2. Right click the game and go to 'Properties'
3. Click the 'Filesystem' tab and right click on any 'Partition #' (Partition 1 usually contains the game data, so try right clicking on 'Partition 1' first)
4. Click 'Extract DOL...' and choose and output folder
5. In the output folder, you'll see that the boot.dol file that's generated is only 1KB in size.

To produce the correct outcome, perform the same steps but scrub the game image of the first partition leaving only the partition with the game's data. The boot.dol file will extract correctly.

Dolphin 3.5 and 3.5-367 are old versions of Dolphin that have
known issues and bugs, so don't report issues about them and test the
latest Dolphin version first.
Which versions of Dolphin did you test on?
Dolphin 4.0-566 (6d63db96e962586b13ad343e26182f9e7be7cc2b) x64
Dolphin 4.0.2 x64

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
Dolphin 3.5 x64

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
OS: Windows 7 Home Premium SP1
GFX Card: NVidia GeForce 680 GTX
CPU: Intel 2500k @ 3.3ghz
MB: Asrock z68 extreme 3 w/ latest BIOS

Are you using the 32 or the 64 bit version of Dolphin?
64 bit.

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
I checked the data inside the .dol file that gets incorrectly extracted from multi partition images and it doesn't seem to be pulling the data from anywhere remotely from the actual .dol file. I was thinking that maybe the data that's getting extracted is just the first few bytes of the actual .dol file or something, but I can't find any reference to the data that's getting extracted anywhere.

The APPLOADER is correctly extracted, though. However, I noticed that when extracting all the files from a Wii image with Dolphin doesn't extract the dol file or apploader, is this normal?

You can download both the correct and incorrect output of Brawl's (NTSC-U) dol file if you're interested here:

http://www.mediafire.com/download/uavx718cpbxgxwg/Extracted%20dols.7z

I also checked the integrity of the disc image with Dolphin on the games I listed and no issues were found.