I found when uploading the BOT plugin for WordPress via FTP transfer that not all of the files completely transferred. The files that I found that not transfer completely were the subfolders of the graph folders. This issue only came to light when the graphs did not display but everything else did display correctly. At first I did not believe there was an issue due to the fact Opera 9.23 and IE 7.0 do not always display images correctly.
My recommendations are as follows
1) a more flatter file directory
2) breaking the plugin into smaller parts to be downloaded and then uploaded
3) finding a way to decrease the number of files that are transferred
4) providing immediate feedback to users if there is a problem with installation