Purely as a hypothetical:
Direct path reads may be overlapping and non-blocking, so there is never any time spent waiting for a read buffer to be filled.
Enabling the level 12 trace may interfere with Oracle's I/O strategy - either making it impossible to dispatch non-blocking reads, or causing file-system/hardware delay that interferes with the non-blocking reads - with the result that enabling the trace causes lots of lost time on I/O.
On another note, enabling tracing at this level on 10.2 also enables _rowsource_execution_statistics, and that can add a massive CPU overhead to certain classes of query (though 3 minutes to 12 hours not likely)
The Co-operative Oracle Users' FAQ http://www.jlcomp.demon.co.uk/faq/ind_faq.html
Cost Based Oracle: Fundamentals http://www.jlcomp.demon.co.uk/cbo_book/ind_book.html