I have read your first post again and I probably need to state my question more precisely: Can you tell whether or not values other than “Absolute path of the media files directory” and “URL of the media files directory” were set back to there default values?
If you install podPress the first time in a blog then the “Absolute path of the media files directory” is empty. Does that value has been set back to the absolute path of the upload path of the blog or was it empty after the upgrade?
Is it right that you have upgraded WP to 3.1 and afterwards podPress to the 8.8.10 RC 5 version? Can you tell whether these values were set back after the WP upgrade or the podPress upgrade?
Basically these settings (and all others too) getting set to the defaults when they are not part of the podPress->settings() array (which is the same as the podPress_config data in the wp_options db table). The procedure which checks the existence of those options gets started e.g. after an version upgrade (when the PODPRESS_VERSION in the podpress.php file is bigger than the version number in the db). But this procedure ignores the “Absolute path of the media files directory” value because the default value is an empty value. The upgrade does not touches this value (the only exception is 8.8.10 RC 10 but RC 11 works as before again). The only action which overwrites this special value is the saving the general settings process.
If checkSettings() function (in podpress_class.php) finds out that the result of the query for the podPress_config value from the wp_options table is no array then it sets the default values. If the result is an array then this function checks whether or not the single elements exist and sets the default values if the don not exist.
Regards,
Tim