Line endings in text files (css & php) going wrong

[Timbow]

I am experiencing a very annoying intermittent problem with finding .css and .php template files either becoming double spaced (or even treble spaced) or losing all line endings so that they are all on one long line. I don't yet know for sure exactly when this is happening but it is at some point in the process of uploading, saving and editing through the GS admin 'Edit Theme' page. I am using Windows XP and notepad++, uploading with Filezilla (set to 'Auto' for text or binary) to a linux server and GS 3.1.

I will need to look more carefully at exactly what is changing and when. It isn't necessarily anything to do with GS, it is to do with the translation of dos/Win line endings to unix/linux and back but has anyone else ever experienced this problem?

Thanks,