Add imported files into sequences using Premiere Pro's ExtendScript connection
Solution 1:
Rather than setting in/out points on the active sequence why not load your raw video into the source window instead, and set the in/out points there, and then build up the final version inside the active sequence.
Copying the clip from Source to sequence can be done many ways and should be pretty easy.
So yea, my advice would be try using source rather than the sequence for clipping. Might have better luck.