Since 2.50, LS use the Yii asset manager:
www.yiiframework.com/wiki/148/understanding-assets/
It moves the CSS files of a theme to a tmp/ sub-directory with a random string (eg: "tmp/1ef64ml/"). So if you make any change to a css file, and tell it to the asset manager, the files are copied to a new sub-directory with a new name so the user browser's cache is updated and they see the new css (else, they would have to clean their browser cache...). Of course, if the Asset Manager doesn't know you changed the file, the old file from the old tmp/directory remain unchanged.
So, when you're editing CSS of a theme you have various possibilities:
1. You can use the the LS Theme Editor: it deals with the asset manager and you don't have to worry about anything
2. You can turn debug mode on: it will turn asset manager off, so the real css/js files of your themes are called (but then, you have to refresh your browser cache at each load)
3. Change (increase or decrease...) the asset version number to refresh all the tmp directories (
github.com/LimeSurvey/LimeSurvey/blob/70...nfig/version.php#L19
)
Using the theme editor to edit the custom CSS is by far the best solution. 
It will help you to understand the architecture of the new theme engine.
Also, if your customizing fruity, be careful with CSS specifity: most of the definitions use the selector ".fruity" (one of the class of the body element)