I'm sorry to hear that you are having difficulties with Showkase.
I'm happy to help if I can but, so far, I have been unable to replicate the problem you reported (with the latest version of Showkase, v1.7.2).
Having created a Juicebox gallery page, with the 'Resize images' checkbox deselected, I uploaded a JPG image.
Immediately after uploading (using the 'HTML5' upload option), the filesize on the server (in the gallery's 'images' folder) was exactly as it should be (identical to the source image).
After publishing, there was no change to the image on the server and its filesize remained constant.
I tried again, this time with the 'Resize images' checkbox selected (but still using the 'HTML5' upload option).
The image was initially resized but its filesize did not change on publishing.
I then switched to the 'Basic' upload option (where 'Resize images' is not supported) and the filesize of the image on the server remained constant throughout the whole uploading and publishing process.
I really do not know what might be causing your problem and, being unable to replicate it makes troubleshooting that much more difficult.
If you are not resizing your images at all (you have the 'Resize images' checkbox deselected), then try both the 'Basic' and 'HTML5' upload options to see what happens using both upload methods. (Maybe the problem happens only with one and not the other.)
Unfortunately, I cannot explain why the image filesizes on your server are changing on publishing and, if your server is somehow contributing to the problem, I do not know what server settings might be responsible.
The first thing I'd do is reinstall the latest version of Showkase (v1.7.2) to make sure that all core files are present and up-to-date.
If you have ever upgraded your Showkase site before, then there may potentially have been some files from older versions on your server (maybe even relating to the upload module) that were not overwritten with the newer versions.
Just follow the Upgrading Showkase instructions with v1.7.2 (even if you already have v1.7.2 installed) and make sure that your FTP program is set to overwrite existing files. (Be sure to backup any 'custom.css' or 'custom.js' theme files beforehand though as they, too, will be overwritten during the upgrade process and will need to be reinstated afterwards.)
I'm not sure that this will help but it's certainly the first thing I'd try.