Very poor insert performance MySQL / Percona Server

Question

I'm running a Percona-Server instance off an Ubuntu server install. I'm using an application that needs to access this database, and its having VERY poor performance. Once the database has been established, the application goes in (upon install) and creates the schema. It defaults everything to MyISAM, however I have converted the table engines back to InnoDB. The issue that I'm having is VERY poor insert performance. This application is very write-heavy, and it seems as though its writing each row 1 at a time to disk, not using any sort of buffers, however I'm unsure how to check or verify this. Even a select(*) from one of the tables will take 2.4 seconds, and there is only 163,000 rows. I'm kind of at a loss as to what else I can do.

Server has 8GB of ram, and CPU is almost entirely idle while this is occurring.

my.cnf:

[mysql]

# CLIENT #
port                           = 3306
socket                         = /var/run/mysqld/mysqld.sock

[mysqld]

# GENERAL #
user                           = mysql
default_storage_engine         = InnoDB
socket                         = /var/run/mysqld/mysqld.sock
pid_file                       = /var/run/mysqld/mysqld.pid

# MyISAM #
key_buffer_size                = 32M
myisam_recover                 = FORCE,BACKUP

# SAFETY #
max_allowed_packet             = 16M
max_connect_errors             = 1000000
skip_name_resolve
sql_mode                       = STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_AUTO_VALUE_ON_ZERO,NO_ENGINE_SUBSTITUTION,NO_ZERO_DATE,NO_ZERO_IN_DATE,ONLY_FULL_GROUP_BY
sysdate_is_now                 = 1
innodb                         = FORCE
innodb_strict_mode             = 1

# DATA STORAGE #
datadir                        = /mnt/Storage/mysql/

# BINARY LOGGING #
log_bin                        = /mnt/Storage/mysql/mysql-bin
expire_logs_days               = 14
sync_binlog                    = 1

# CACHES AND LIMITS #
tmp_table_size                 = 32M
max_heap_table_size            = 32M
query_cache_type               = 0
query_cache_size               = 0
max_connections                = 500
thread_cache_size              = 50
open_files_limit               = 65535
table_definition_cache         = 1024
table_open_cache               = 2048

# INNODB #
innodb_flush_method            = O_DIRECT
innodb_log_files_in_group      = 2
innodb_log_file_size           = 512M
innodb_flush_log_at_trx_commit = 0
innodb_file_per_table          = 1
innodb_buffer_pool_size        = 6144M
innodb_buffer_pool_instances   = 1
innodb_read_io_threads         = 64
innodb_write_io_threads        = 64
innodb_io_capacity             = 10000

# LOGGING #
log_error                      = /mnt/Storage/mysql/mysql-error.log
log_queries_not_using_indexes  = 1
slow_query_log                 = 1
slow_query_log_file            = /mnt/Storage/mysql/mysql-slow.log

desc of one table that is having poor insert performance:

mysql> desc parts;
+------------+---------------------+------+-----+---------+----------------+
| Field      | Type                | Null | Key | Default | Extra          |
+------------+---------------------+------+-----+---------+----------------+
| ID         | bigint(20) unsigned | NO   | PRI | NULL    | auto_increment |
| binaryID   | int(11) unsigned    | NO   | MUL | 0       |                |
| messageID  | varchar(255)        | NO   |     |         |                |
| number     | bigint(20) unsigned | NO   | MUL | 0       |                |
| partnumber | int(10) unsigned    | NO   |     | 0       |                |
| size       | bigint(20) unsigned | NO   |     | 0       |                |
| dateadded  | datetime            | YES  | MUL | NULL    |                |
+------------+---------------------+------+-----+---------+----------------+
7 rows in set (0.00 sec)