Emulator

What's the problem? Describe what went wrong in few words.
Dolphin currently doesn't write GCI Folder saves to disk until you stop emulation from within Dolphin. If Dolphin crashes or is forcibly closed in some way that prevents the normal emulation stop code from running, any changes to .gcis are lost.

I lost about two hours' worth of Pikmin 2 progress last night because I had to force-quit Dolphin after I made the unfortunate mistake of checking Render to Main Window for the temporary convenience of having the log next to the render window, then going into fullscreen and realizing that that currently breaks all keyboard shortcuts. Fucking Armada and his exclusive fullscreen, causing issues while likely providing zero benefit on OS X. v_v

What did you expect to happen instead?
I expect a whole Dolphin to fly out of my screen and write .gci changes to disc within, say, five seconds of a game writing to memcard. With its girthy goddamn tail.

What steps will reproduce the problem?

1. Open Dolphin, make sure you're using a GCI Folder, start up a GameCube game that saves to memcard.
2. Play that game (make noticeable progress!) until it saves to memcard, then forcibly kill the Dolphin some time after it's saved.
3. Reopen Dolphin, reopen that game, notice that your progress ain't there anymore.

Which versions of Dolphin did you test on?
new-zelda-hle 4.0-4883. Present in master as well, and there haven't been any GCI Folder-related changes in a month or two.

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?
This has likely existed as long as GCI Folders have, and if it's a regression I really don't care to bisect for it.

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
Mac OS X 10.10.1, iMac 11,2
Intel Core i3-540 (3.06 GHz, 2 cores + hyperthreading, Nehalem)
ATi Radeon HD 4670 (256 MB)

This also affects Windows (as JMC47 confirmed) and should affect Linux/Android unless we're using OS-specific file access code. I don't know if this issue occurs with raw memcard files.