Thanks for letting me know - this was caused by a change on the AFF website. It's fixed in v1.0.47 and newer.

Please contact me via www.ficlab.com/contact for assistance with troubleshooting your issues. The indents in particular are more likely to be a bug in your reader app; FicLab doesn't add paragraph indents in the chapter text unless it's configured to do so.

If you dislike the way the covers work, it would be useful if you could let me know what it is about the covers you object to - I'm generally fairly responsive to user feedback on that kind of thing.