Enabling "log_queries_not_using_indexes" disables "long_query_time"?
That is expected behavior.  Refer to the docs online, but in summary:


long_query_time is the threshold for query execution time beyond which it is logged.  Any queries taking longer than the threshold are logged, regardless of whether they use an index or not.
log_queries_not_using_indexes tells MySQL to additionally log all queries that do not use an index to limit the number of rows scanned.  Logging on this condition happens regardless of execution time.


Hope that helps explain what you are seeing.  It seems like you probably just want long_query_time and not log_queries_not_using_indexes if your goal is to only capture queries that take longer than a particular threshold.

Doc links:
http://dev.mysql.com/doc/refman/5.5/en/server-options.html#option_mysqld_log-queries-not-using-indexes

http://dev.mysql.com/doc/refman/5.5/en/server-system-variables.html#sysvar_long_query_time