I too have been having this problem since 0.14. I'm on a Mac.
Here's an example...
1. I download Cory Doctorow's "Down and Out in the Magic Kingdom" from Feedbooks. (I have this problem with any epub or html with indents)
2. Open in Adobe Digital Editions and indents are there (see Picture 1).
3. Open in Sigil 0.15 Mac and indents are gone (see Picture 2).
4. Make small edit (girlfriend to boyfriend) and resave as epub.
5. Open the new epub in Adobe Digital Editions and indents are gone (see Picture 3).
Also attached are the original and resaved epubs.
NOTE: In a few cases where I've opened html files in Sigil, the indents show but don't save.