Well, I haven't had any problems using TRIM 'til now... I usually do the COS Projection on an ortographic view (ie. side, top, front, etc...), when I use the Trim tool I firt select the NURBs surface (most of the cases a sphere with 2 COS resulting from a projection), then select the trim tool, at this point you should pay attention to what the status bar says, it provides you with information about the tool, what portion must you click, to select which part will remain and which one will be trimmed away. If you're having trouble selecting the projected COS that you want, try doing a zoom and pick the one you DON'T want (before doing any trimming), erase it or hide it and next time you pick on a COS you'll be sure that you're picking the correct one.
Hope it helps.