I have gone through all the settings and configured to my requirements. However, I already have an htaccess file and so only ever saved without creating the htaccess file.
Because I had problems with the first website, when it came to the second website I put the following text in "Custom .htaccess rules at the top of the file"
######top rules##########
I did the same for the bottom and clicked on Save without creating htaccess. All data was retained. And so I went to my existing htaccess file and copied the rules that I wanted to put into the top of the file and the same with the bottom and pasted them into the fields in htaccess maker. Then clicked on Save without creating htaccess. This is where the problem happened. ALL fields were reset to their original settings and the data in the two htaccess custom rule fields were removed so they were blank. I could then repeat the process but when copying my htaccess data into the fields again, all data was reset and lost again.
Here is an example of one of the lines:
RewriteCond %{QUERY_STRING} ^ID=75$
RewriteRule ^news\.asp$ http://www.website.co.uk/council-news/? [R=301,L]
Can you replicate this? I'm nothing amazing when it comes to diagnosing such problems, but I guess some of the characters in the Rules might be causing problems with your script when updating the database?
I see this person had the same problem
http://www.akeebabackup.com/support/forum/topic.html?id=26343