This appears to be a bug in SC2 when using a Realtek soundcard.
Here are two threads on battle.net from users experiencing the exact same problem. The issue seems to be that, when Starcraft II first starts up or first loads a map, it sometimes arbitrarily changes your mic volume and mic-boost settings to whatever it feels like. The reason it doesn't last is that Skype is smart enough to reduce the volume again when it detects how loud it is.
Here is an ironically quiet video demonstrating the issue. The thread that video comes from has a potential solution, which seems to work for some but not others:
Open your in-game options and go to the Voice tab. Here’s the settings your game uses to interact with the mic.
Change the Settings in the Talking section (you’ll need to Enable Talking first if it’s not already):
- Select the correct Input Device (default device will be picked by default).
- Adjust the microphone volume to whatever you want your mic set at.
- Uncheck everything (unless you actually use the Voice Chat).
As a side-note, that same thread also has a solution for another annoying problem us skyper's face: when starting a game during a call, skype (Actually, it's Windows) will sometimes reduce that game's volume.
The solution is to change the setting under control panel --> sound --> communications