Mysql load from infile stuck waiting on hard drive
Your bulk insert buffer is 4G. That's great ... FOR MyISAM !!!

InnoDB does not use the bulk insert buffer.

You may need to have sqlalchemy throttle the load data infile calls into multiple transactions.

You may also want to disable innodb_change_buffering, setting it to inserts.
 Unfortunately, you cannot do SET GLOBAL innodb_change_buffering = 'inserts';. If you dom you may need to set it in my.cnf and restart mysql.

UPDATE 2012-07-13 16:53 EDT

I just noticed that you have two values in the my.cnf for innodb_buffer_pool_size. First one is 2385M, and the last one is 14G. If MySQL for Windows accepted 14G and you only have 12G of RAM, your server must be having a good old time swapping.

You can verify what the buffer pool size is with

SHOW VARIABLES LIKE 'innodb_buffer_pool_size';


UPDATE 2012-07-13 16:58 EDT

You may also want to check how full the buffer pool is with this

SELECT FORMAT(A.num * 100.0 / B.num,2) BufferPoolFullPct FROM
(SELECT variable_value num FROM information_schema.global_status
WHERE variable_name = 'Innodb_buffer_pool_pages_data') A,
(SELECT variable_value num FROM information_schema.global_status
WHERE variable_name = 'Innodb_buffer_pool_pages_total') B;