The problem appears to be that Microsoft Speech Recognition is using old microphone levels from when it ran the microphone configuration wizard in the past. Each time the program opens it resets the microphone levels to this stored value.
Go to Control Panel > Ease of Access > Speech Recognition. Click "Advanced speech options" in the sidebar on the left side of the window. A new window should pop up, called "Speech Properties". In the bottom right of that window, click "Configure Microphone", and it should start the configuration wizard which will have you speak a phrase and adjust the microphone for speech recognition accordingly.
Hopefully that solves the problem.