Hi,
I have this custom search url: secure.gooddata.com/#s=/gdc/projects/{query}|dataPage| (I removed https:// from the beginning of the link so that your WYSIWYG won't interpret it as url) and it doesn't work. Alfred identifies the search but not open it in browser after hitting Enter (Test button in Search Edit Preferences doesn't work either).
I use Alfred 2.0.2 (178) on Mac OS X 10.8.3 and it worked in Alfred 1.
Thanks.
Jakub