While I am a bit unclear in my understanding of what you are saying, my recommendation would be as follows to see if you get a better result....
Instead of using an 'Export' function, choose 'Save File As' ...
To delete a portion, pinpoint the cursor on the spot where you wish to begin your delete, and drag to the end of the selection you wish to delete. Once a selection is made you can zoom in and use the I< and >I transport buttons to adjust/verify that the beginning and end points are where you want them. Then 'delete' the selection. It's good practice to use 'Save File As' so you keep the original file intact.
ps. just curious, are you working with a wav file or an mp3?
edit to add: This turns out to be a VideoPad topic - my responses were aimed at WavePad....