Hi,
Let me start by saying that i feel I am doing something wrong 
I am facing similar (but not identical) issues that are described here
http://forum.piwik.org/read.php?2,71952
I definitely see some of my goal tracked. I see the web logs and all goes ok.
From historical reasons I am using server side HTTP call to track this goal. This is a purchase action and I have a goal defined for that and sending a server-to-server URL like
/piwik/piwik.php?rec=1&apiv=1&idsite=427&idgoal=3&rand=565514&revenue=1399.00
In the piwik_log_conversion table I see a fraction of my goals there - some goals have the same idvisitor - which is kind of strange as from a server-to-server call (no browser) I do not send any cookies. Just wanted them treated as separate visitors/visit for every call.
I saw the limit of 1 conversion per visit - but as there should not be user id on the call I was expecting each to be treated as separate visit anyways.
Question is - through this method where did my goals disappear?
Thanks,
Arie