@Bill, I don't know what to tell you, but I experienced that problem repeatedly between WP 2.9.2 and 3.2.1, as I was converting a bunch of sites to use Genesis. I had custom rules in between the # Begin and # End that were "erased" from existence, and I had them outside the # End and they still were obliterated, both scenarios leaving me with the "default" rewrites to handle the permalinks and nothing else.
It happened so much I changed the permissions on the file so that it couldn't be overwritten by WordPress. So the permalinks rules were being written, if that's what you're suggesting, but I also had my custom rules (the comments ones and the ones to prevent image hotlinking) wiped out of my .htaccess files on as many as 6 different websites several times over a 2 year period. I just got into the habit of keeping a copy of my rules in a separate file, and just pasting them back in whenever I had to click "Save Changes" in the permalinks section.
I'll test it out eventually, but I'm in the middle of a couple of projects and in no rush at the moment to debug. Sounds a lot like my wp-uploads settings problems that no one else but me had, either
@Summer - Anything between the # Begin and # End will be wiped out. That's the expected behavior. The rest of what you experienced isn't, so it's either caused by your server setup, themes, plugins, etc. But it's not caused by default WP. Although our servers don't run Apache, I've used Apache with WP often enough to know that what you're seeing isn't the norm.
When you have the time, give it another look. If there's something odd about your server setup, it will probably strike you at other times down the road when it's less convenient.
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