Emulator

I assume setting fullscreen resolution to something other than auto fixes it?

I am unable to set it to any other resolution on my system. Auto is the only option.

Um...was there no options at all before?

When reverting to 3.5-1344, the full screen resolution shows "No Resolutions Found", and changing the window size works again.

Enhancements > Internal Resolution > Auto (Window Size) seems to be malfunctioning a little bit I think. If I choose another option and then go str8 back to Auto (Window Size), it will work properly but will have to do again on emulator restart. My resolution is 1080p and fullscreen rez is on auto and internal resolution is on auto.

Currently, when emulator is fullscreen, the internal resolution isn't autoing to 1080p unless I change the internal rez option and then turn it back to auto.

I have same problem.
Try to maximize dolphin window and then launch game.

I have the same issue. I bisected to commit 2697b8c04f9e7c8d0a40bd42db95b4a534947c43.
The following error is emitted from my system when I try to go fullscreen:
(dolphin-emu:21328): Gdk-WARNING **: /build/buildd/gtk+2.0-2.24.13/gdk/x11/gdkproperty-x11.c:325 invalid X atom: 3122107072
I also get a whole bunch of GL driver warnings about invalid Uniform Locations, but I feel like those are unrelated.
This is on a Gnome3 windows manager on Ubuntu 12.10
Intel HD4000 graphics card
But from the warnings, it looks like it's just an error with the way you are using X, so it should happen on all Linux systems.

I can confirm the issue for version 3.5-1410 running un Ubuntu 13.04 x64.
The option "Use Fullscreen" is the only fix that works for me.

The black window is rendered, the rest is just plain white for me:
http://screencloud.net//img/screenshots/e63beaaa2acb9c9543025612a587fcd5.png

Just writing here to confirm this issue, happens on Slackware 13.37 x64. I've a GTX 550 Ti as well.

After fishing around a little, it seems that the issue is actually with the commit ca12e7ee8f05da66743abe0d9826a7d145e8b28e, which makes sense as that one actually has something to do with fullscreen. The reason that my bisect was messed up before must have had something to do with the default settings changing while I was bisecting.

This seems to not be implemented properly. Changing the fullscreen resolution myself in the settings makes fullscreen work, but it still emits warnings about invalid atoms.

matthew, are you sure? I was trying to pinpoint the error to a specific revision, and I've gotten the same issue with fullscreen as early as 7c50ac931d79be9e1f4d62053af3764fdf93e9d6, but fullscreen works as expected in 48f3e962d6e10578813f12b8edfd7b6e06000620. The issue seems to have been introduced somewhere within those 100 commits. Note, I'm just trying to find revision ranges where the issue does and does not occur, so I can eventually narrow it down.

So, setting fullscreen resolution to something other than Auto fixes it in latest master? Someone else said it didn't, but the behavior is exactly the same as before if it's not, so something doesn't add up...

Does reverting revision 2697b8c04f9e7c8d0a40bd42db95b4a534947c43 work? I haven't tried fullscreen, but resizing my window works now ...

Alright, I've located the commit where this was introduced: 05eda7b0c1c71a0d5f76a4690060419f00a78ce5

The previous master branch commit runs just fine on Linux: 0973d503efbd140594350a73ee30b6f4bf0a5934

Also rachel, setting the fullscreen resolution to anything other than Auto does not solve the issue (at least not for me). I'm using the latest master branch revision as of this writing: 02cbcc8ec49676739315223b8d2b0867867f7352

The problem is the same before and after an Auto option was added for fullscreen resolutions.

Yeah. I don't know how I got confused back there, but the current master with 2697b8c04f9e7c8d0a40bd42db95b4a534947c43 reverted works for me. From the commit message it sounds like you know what was going wrong, so hopefully that commit can be implemented without breaking anything.
Thanks!