According to Freecoder:
Eliminates Silence
Freecorder Toolbar starts recording when it first detects audio, and stops when audio stops. Now you never have "dead air" at the start and end of your recording - it's perfect every time!
I don't know if this is what is happening.
Also, check your settings:

Try a recording in WAV format. WAVs are much easier to write to your hard drive as there is no complession involved. Writing to MP3 may cause the PC to stall as it is a much more CPU intensive process.