I had the same issue as in this thread. I was going to comment there but the forum said to start a new thread rather than reviving that one.
The issue seems to be that when the Windows service is created the path is set as;
d:\winids\snort\bin\snort /SERVICE
But it should be;
d:\winids\snort\bin\snort.exe /SERVICE
In the registry go to HKLM\SYSTEM\CurrentControlSet\Services\SnortSvc then edit the ImagePath entry to change the path