I've tested the upgrade of the community site on nginx and not having this issue, so it's not nginx specifically.  I used the rewrite rules Pawel posted in another thread that I think Ura used too.

i will not be retesting 1.9 with a fresh instal here, since i am not intending to use ckeditor anyway... unless i find other, similar glitches with other code/plugins.

i used Pawel's rewrites, yes.

the upgrade process was to delete all files/folders except for the plugins i was already partway through porting to 1.9. copy in the rc1 version of elgg. update the settings.php file. update the nginx config. ran the upgrade.php file.