Emulator

What's the problem?
In many aspects the emulator seems to be running at two times normal speed. I first noticed this a while back, when I looked at the RTC in the GCN IPL. It is showing almost the correct time (it's a couple minutes slow), but it seems to be counting two seconds for every real second. At the time I didn't think much of it.

Then I tried playing Super Smash Bros. Melee (either selecting it from the menu or after the little cube rolls around), and it was the same story… The match timer ran at 2x speed, and so did the entire game. But the FPS and VPS counters both showed 60FPS and it says it's going only 100%.

I tried everything I could think of. Framelimit set to "auto", framelimit set to "60 (FPS and VPS)" and I even tried audio throttle in the DSP plugin. The only workaround I found was setting framelimit to 30.

Dolphin version with the problem (as it appears in the title bar, Ex.: "R
4779" or "R 6403M"):
r6486

(optional) Dolphin version that does not have the problem:
Well I got sick of testing but this has been happening since at least r6353 (probably much longer).

Operating system and version: Windows XP
32-bit or 64-bit: x86

Game ID (as it appears in game properties, Ex.: "GZ2P01" or "RSBE01"):
Any, but for SSBM it was GALE01

Was the ISO a plain dump from disc, compressed and/or scrubbed?
It's a raw ISO dumped from my disk.

Please provide any additional information below.
Dualcore, singlecore, idle skipping, none of it matters.