Slowness for Inserts/Updates hanging on 'closing tables' and 'freeing items' (no replies)

I'm moving an existing 5GB database to a new server (Intel quad core, 8Gb RAM) with software RAID 1 disks, CentOS 6 and MySQL 5.1.52-64 bit installed. The normal CLI import of the database onto the new server went off without a hitch, no significant delays on the INSERT statements.

However, when doing a large batch update via a PHP (5.3.8) script that includes updates to INNODB tables and inserts to MyISAM tables, a few hundred or thousand records will process quickly for about 2 to 10 seconds and then all of a sudden get hung up on a single insert or update. The hangups mainly occur for MyISAM tables (inserts) on the status 'closing tables' and for INNODB tables (updates) on 'freeing items'. The hangup last from 2 to 20 seconds and then things proceeds normally. There is no other activity on the server.

I thought the problem might lie with the software RAID, so I did some random access read/write tests (shown below). But the setup performs slightly better than my test server. Also, I can run this same batch update on my test box (an old box with 2GB ram and with almost the same my.cnf) and see the same effects, though the hangups are significanly shorter and less frequent. However on my Windows development laptop I see no problems at all.

FYI, there seems to be no problem with normal SELECTs. They proceed without hangup and I can get 4,000 to 5,000 a second on tables with millions of rows. My test box and Win7 laptop with the same benchmark test get 3,000 to 4,000. The inserts/updates in question are the simple single table variety. Eg: INSERT IGNORE INTO some_myisam_table (fld1, fld2, fld3, fld4, fld5) VALUES (val1, val2, val3, val4, val5). And for updates: UPDATE some_innodb_table SET field='abcd' WHERE key=12345. The tables they are operating on have between 1 million to 20 million rows and three or four keys per table.

It almost feels like server is flushing a cache ever few seconds when I see a single update hanging, and then proceeding normally. I've poured over the my.cnf as well as searched all potential bugs online. Any thoughts?

## HD READ RANDOM ACCESS TEST (done with SeekMark - http://learnitwithme.com/)
## -----------------------
## Threads: 2
## Seeks: 1000
## Read from File: test.file (4.8Gb)
[mm@server]# ./seekmark -t2 -s1000 -f ./test.file

READ benchmarking against ./test.file 4834 MB

threads to spawn: 2
seeks per thread: 1000
io size in bytes: 512

Spawning worker 0 to do 1000 seeks
Spawning worker 1 to do 1000 seeks
thread 1 completed, time: 6.03, 165.92 seeks/sec, 6.0ms per request
thread 0 completed, time: 6.41, 156.01 seeks/sec, 6.4ms per request

total time: 6.41, time per READ request(ms): 3.205
311.96 total seeks per sec, 155.98 READ seeks per sec per thread

## HD WRITE RANDOM ACCESS TEST
## ------------------------
## Threads: 2
## Seeks: 1000
## Write to File: test.file (4.8Gb)
[mm@server]# ./seekmark -t2 -s1000 -w destroy-data -f ./test.file

WRITE benchmarking against ./test.file 4834 MB

threads to spawn: 2
seeks per thread: 1000
io size in bytes: 512
write data is randomly generated

Spawning worker 0 to do 1000 seeks
Spawning worker 1 to do 1000 seeks
thread 0 completed, time: 38.95, 25.67 seeks/sec, 39.0ms per request
thread 1 completed, time: 39.10, 25.57 seeks/sec, 39.1ms per request

total time: 39.10, time per WRITE request(ms): 19.552
51.14 total seeks per sec, 25.57 WRITE seeks per sec per thread


## MY.CNF
## ------
[client]
port = 3306
socket = /var/lib/mysql/mysql.sock


[mysql]
default-character-set=utf8
no-auto-rehash 

[mysqld]
port = 3306
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
symbolic-links=0   
character-set-server=utf8
max_connections = 250
max_user_connections = 40
key_buffer = 384M  
myisam_sort_buffer_size = 64M 
join_buffer_size = 2M
read_buffer_size = 2M
sort_buffer_size = 2M  
table_open_cache = 1024
thread_cache_size = 16
wait_timeout = 120
connect_timeout = 10
max_allowed_packet = 4M   
max_connect_errors = 10
tmp_table_size = 16M
query_cache_limit = 1M
query_cache_size = 64M
query_cache_type = 1  
myisam_max_sort_file_size=40G
read_rnd_buffer_size=8M  
innodb_additional_mem_pool_size = 20M
innodb_flush_method = O_DIRECT
innodb_log_buffer_size = 4M
innodb_buffer_pool_size = 2048M 
innodb_log_file_size = 256M  
innodb_thread_concurrency = 32 
innodb_flush_log_at_trx_commit = 2 
log_output = FILE
slow_query_log = 1
slow_query_log_file = /var/log/mysql-slow.log
long_query_time = 1

[mysqld_safe]
open_files_limit = 8192
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

[mysqldump]
quick
max_allowed_packet = 4M

[myisamchk]
key_buffer = 256M
sort_buffer = 256M
read_buffer = 2M
write_buffer = 2M

[mysqlhotcopy]
interactive-timeout