Were you trying to use a plugin to manually process the new rewrites you generated? If so, and you were trying to access new query variables, WordPress 2.0 requires that you use the query_vars array instead of the standard $_GET method. This is not very well documented anywhere – at least not the last time I looked, so it can be frustrating trying to figure out why you cannot pass new custom query vars (with or without permalinks). :)

You also have to use a filter on the ‘query_vars’ event to actually add the new query field in, or it will not be recognized by WP either.

If you want an example of custom query parameters, you can view the source of my sitemap generator plugin on my site.

Of course, none of this may apply to you anyway – just thought I would share just in case :)