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By default, Kickstart extracts the .htaccess file as htaccess.bak. When you click the second link it tries to rename it back to .htaccess. Two issues here. The first is having adequate permissions of doing that, as well as having a server which really allows a PHP script to create .htaccess files (some servers deny writing to this file!). The second issue is that since it's a hidden Linux file, it may not appear on FTP and host's control panel file manager even though it's there. Even forcing display of dot file doesn't work. In such a case you can try connecting to your site's root with FileZilla, then perform a manual file transfer for .htaccess. Even though it's invisible, FileZilla downloads it properly! It's 100% counter-intuitive, but I've seen that on too many servers. It's not a Kickstart bug, it's the system administrator's rules applied on the FTP server configuration ;)

Hugh,

it's great to know we're on the same page! OK. What I have discovered is that some hosts do not allow creating any file whose name is .htaccess, unless you rename an existing file. Presumably, they want to protect their server from hackers who might be tempted to do funky redirections on the .htaccess level. However, there was no server which refused uploading a .htaccess file. This brings me to the obvious question: is there a .htaccess (not htaccess.txt) file in the backup archive? Kickstart will not rename htaccess.txt to .htaccess, on the grounds that if you really needed a .htaccess you should have created one. Furthermore, many people restore to WAMPserver and XAMPP. By default, they don't have mod_rewrite enabled, so you can imagine what would happen when a user who can't spell SEO tried to restore his pretty basic site to a local server, right? If .htaccess is indeed included in the archive, you have clicked both links in Kickstart's final page (the second link finalizes the restoration of .htaccess) and it still doesn't show up then I have to look into it.

@bwakeeba - Upgrade to 3.0.a2.1 to make the problem go away, then go to Configuration and click on Save. This should be enough. I am still working on the documentation. Expect a draft documentation release by Friday.

You can extract the JPA archive locally, using Akeeba eXtract Wizard (it even runs under Linux with WINE and Mac OS X using DarWINE). If the .htaccess file is in there, the problem is that during the archive extraction Kickstart wasn't able to rename htaccess.bak (the dummy name it uses when extracting .htaccess) back to .htaccess. This happens if the server's root isn't writable to the web server's user. I usually don't run into this problem as all my sites are hosted in Rochen, which uses suPHP and, as a result, no such thing as ownership issues have ever bothered me :)

@BWakeeba Um... are you sure? Line 47 in the new version is a closing curly bracket, so there's no way you can get this error message. Please double check that the version is 3.0.a2.1. If it really is this version, go to Configuration and click on Save - even without changing any setting. This should work. But, please, double check the version. I think that you accidentally installed 3.0.a2. Granted, they differ in the sub-sub-minor version number, it's easy to do that mistake (I plea guilty; I did that on one of my sites).