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I have the same issue and it is driving me crazy.
Edit: I should have included that I'm using Windows 7 with all of the latest updates.
Edit: I should also include that when I am editing the snippet, it looks properly formatted.
It only gets modified to replace carriage returns with comma's after I drag it to the SQL editor.
This issue has already been reported and fixed for the upcoming 4.0.2 patch. The bug is actually in a Published status, so I'll reference it here:
Bug 18337766 - MULTI-LINE SNIPPETS - CARRIAGE RETURNS REPLACED BY COMMAS WHEN SENT TO WORKSHEET
Thank you for the update. I'll download the latest version and hope to get this fixed.
I thought I'd also note in case other review this that this issue seems to extend beyond just snippets.
If you drag SQL criteria from one location in a where clause to another it will drop a comma after the newly dragged criteria for some reason. I'll check to see if this issue persists after the update but I think they may be related. If the issue persists, I'll open a new thread.