I'm having the same issue on my first Joomla install (on IIS no less). Sadly, this could be a deal breaker for what we're hoping to use Joomla for.
I'm using Joomla 1.5 and everything seems to work great except for this one issue. Technically I could manually edit the dates to force the behaviour I'm after but with the number of articles I expect to be entered into the system, that's a sub-optimal solution and we may be better off publishing manually via Dreamweaver.
The basic premise is we need to document our compliance or noncompliance with a checklist of institutional effectiveness goals. I'm hoping we can also put in some additional functions, but right now that's the extent of what I'm testing. So I have "compliance narratives" set as a section with the other possible functions defined as other sections but currently left unpopulated.
The effectiveness goals are split up into different areas, and these fit neatly into categories. Each of these areas have a checklist of goals, and the items on the checklist correspond to the articles in our current set up. The full checklist ends up being broken down into numbered areas each with numbered check list items. So we have an item 3.7 for example, which would correspond to article 7 in category 3 of the compliance narrative section. The logical way to enter everything would be to start at the top of the list and create the article and drop them into the proper categories within the current section. But doing this produces the exact opposite order from that desired. I could tell people to instead start at the bottom of the list and work up, but that's counter intuitive and I'm dealing with a fairly techno-phobic group (Joomla's user friendly reputation is the primary reason I'm testing it out). Also, each area will have a different person or possibly even a team of persons working on it simultaneously. Starting on area 2.x at the bottom and working up is viable for one person being responsible for that content, but if there's at team it severely limits the ability to work in concert on content creation without the risk of jumbling the content order.
In theory all the articles could be created by me (from the admin account) in whatever order we need and then the people creating the content could just edit rather than create those article from scratch. But this seems like a hack and looses quite a level of agility in adapting to changing content needs. It may also be possible to step the categorization process either forward or back. Area 2.x could be a single article with page breaks between 2.1 and 2.2, for example. But that could create the need for multiple people to need to edit the same article in order to meet deadlines and I'm not sure how Joomla handles such situations. Stepping the scheme back means we'd lose the ability to use Joomla for any of the other high level functions currently defined as sections.
The best possible solution is to get the article order displayed in the article management screen to behave in an intuitive way. So far it seems the only way to do this is to create custom menus for everything, but that defeats the purpose of using the Section Layout menu type.
Any assistance anyone can offer on this would be GREATLY appreciated. I need to have my Joomla proposal in a demo-able form by the end of the week in order for it to receive any real consideration by the decision makers in my organization. This seems to be the only hurdle in the way and I may just be making a typical newbie mistake.
The option I gave only works if you use the menu item to get to the category. 
