Is your output facing your conduit? I actually had to try because i didn't think it would be an issue but if the output face of your outputbus is facing anywhere but the conduit or which ever extraction method you are using, you won't be able to take out items from it by automation.The input bus on the EBF seems to work without issue with automation, and even when I'm standing in front of it, it won't output correctly for numerous hours. :/
On the other hand, when doing so manually, this is not an issue.