what type of file was you working with originally?
also,are you now saving it as a lossless file?
try saving it as the same type of file/bit rate as the original.
i had an mp3 at 192kbps that was about 4.3MB. i removed less than 1 second at the beginning,and about 3 seconds of silence from the end.the end result was a file of approx. 4.2MB.
you two must be doing something wrong somewhere.