yeah, FCP does not trim media to add a transition.
you have to do that yourself
if there isn't enough handle FCP trims the transition.
if there is no handle you cant add the transition.
"The first transition, a dissolve from a black slug to the first clip gave me a drop frame warning and has a nasty jump at the completion of the transition."
does it need rendering?
"The rest of the sixty+ clips are on the timeline and rendered-it took about an hour to render them"
you need to transcode your footage to an FCP friendly format.
that might take about the same amount of time,
but could be quicker if compressor is set up correctly.
however, once the footage is a format FCP likes, then it will be much easier to work with.
what you convert to depends on what version of FCP you are using, and what you plan to do with the footage.
nick