I am also experiencing strange issues with custom agenda commands after I upgraded to 7.8.10 (not sure if from 7.8.09 - I might have skipped a version or two).
In my case the negative tag selection stopped working in tags-todo. For example, "project-somedaymaybe/!TODO" works as if it were "project+somedaymaybe/!TODO" I haven't found time yet to narrow down the configuration and org files to something resembling a bug report. >> Did something change recently in the agenda construction related to >> tags-todo? > > This: http://orgmode.org/w/?p=org-mode.git;a=commit;h=c50f0c I will try to see if reverting this helps in my case. -- Laurynas