I noticed this problem a while ago but it never really bothered me much until the feature was added to display the total downloads next to the actual download link on the post itself. Because of that, I decided to look into why the numbers were so small and while checking out the mysql database tables, I found that there were duplicate entries in the podpress_statcounts table. After checking the media names column I found that all of my media file names contain parentheses () in them. It seems that because of this, there were two rows created for each podcast media file. One row with a media name containing the normal parentheses () and another row with the parentheses replaced with URL encoded values of %28 and %29 instead of the ( and ) from the first row. Since I have Full Stats enabled, I also checked the podpress_stats table and found that this problem did not happen there. That table only contains entries with the normal () and no URL encoded parenthesis values.
This issue seemed to start at least of few updates ago. I didn't always update when there was a new version, so I'm not sure of the exact version number, but I believe it was when enhanced stats features were added.
Here is a small portion of the most recent rows from the podpress_statcounts table:
"postID","media","total","feed","web","play" 126,"Ketonom%20-%20Moon%20Phase%2004%20%28320k%29.mp3",6,0,2,4 126,"Ketonom%20-%20Moon%20Phase%2004%20%28192k%29.mp3",22,0,2,20 126,"Ketonom%20-%20Moon%20Phase%2004%20(192k).mp3",1983,9,1486,488 126,"Ketonom%20-%20Moon%20Phase%2004%20(320k).mp3",1740,3,1567,170 132,"TFCM04%20-%20Ketonom%20(320k).mp3",214,7,191,16 132,"TFCM04%20-%20Ketonom%20%28320k%29.mp3",2,0,0,2
Of course, these additional rows also show up when viewing the podpress stats from the wordpress administrator panel as well.
I should also note that postID 132 was created just recently while I was on podPress version 18.104.22.168 (I think). I just upgraded to 22.214.171.124 right before posting this.