my files randomly get minified (no caching plugin)

When I upload files via ftp to the WordPress theme or a plugin folder, they sometimes get minified in a bad way — code gets pushed onto one-line comments, spaces are automatically added after a colon (goodbye pseudoclasses), etc. Basically, my code gets destroyed and won’t even run in this state. This happens inconsistently — I can’t always reproduce it, though it only occurs when I upload a new file.

Also, another less-pressing problem is that if I view a .css file in WordPress’ editor, it basically adds a line break to every other line. This isn’t viewable in the WP editor the first time, but if I download the file via ftp and view it in my text editor it is apparent. My 2000-line css files get magically turned to 4000.

No plugins are installed in WordPress besides a .less compiler (problem happens even if I don’t use this).

I am using NotePad++ and WinSCP and am wondering it it’s an encoding problem. UTF-8 without BOM, or ANSI doesn’t seem to make a difference though. The problem also happens when I use FileZilla (transfer type is set to auto).

Before I smash my computer and jump out this window, I’m curious if any other folks have run into anything like this.