Hi Rafael,
It looks like you may have another example of WordPress interfering with the CSS file … https://geek.hellyer.kiwi/forum/index.php?topic=177.0
What permalink structure do you have? For some bizarre reason, the permalink structure of WordPress seems to be interfering with the interaction of the CSS file with the WordPress database on some hosts. I can’t replicate the problem, hence haven’t been able to find a solution to it. I have no idea how to fix it, but if you can think of any possible reasons why you may have this problem on your host I’d love to hear.
Actually, on second thought, it may have something to do with your permissions settings. What are the permissions settings for your style.php file (in plugins folder)?
In the mean time, you can fix the problem by upgrading to the new Multi-level Navigation Plugin and choosing the ‘disable css’ option in the admin page, then entering your CSS directly into your themes CSS file.