MYSQL 运作一小段时间后，速度变得奇慢。而CPU基本空闲状态

mysql 运行一小段时间后，速度变得奇慢。而CPU基本空闲状态！
【运行环境】：
WIN 2003 + APACHE2.2 + PHP5 + MYSQL 5.1.54

【服务器配置】：双核2.2G主频；1.5G内存；150G硬盘
【数据库情况】：
1. INNODB，ibdata 有30G
2. 有近2万张表，表的字段比较少（基本上10几个字段，最多有40个字段）；
3. 大部分表的记录数，不超过3万条；只有个别表的记录有百万条的数量级。

【数据库使用情况】：
1. 连接只有几十个，其中，有几个连接是后台守护程序在用，查询和写入的频率很高（类似实时系统）。

【问题描述】：
1. 在MYSQL控制台下面，不管是什么操作（查询/更新），都非常慢（一张1万条记录的用户表，查记录数都要几秒~几十秒）。而此种情况下：mysqld占用约500M内存，CPU基本上都是2%（好像不工作）。重启MYSQL后，稍微好一点，但不一会，又开始很慢。
对比：最奇怪的是，之前的速度比较正常，mysqld 占用约500M内存，CPU占用50%，MYSQL查询速度比较OK（都是0.0X秒）。

我是MYSQL菜鸟，请大虾指教，是什么原因？

附：MYSQL配置：
# MySQL Server Instance Configuration File
# ———————————-
# Generated by the MySQL Server Instance Configuration Wizard
#
#
# Installation Instructions
# ———————————-
#
# On Linux you can copy this file to /etc/my.cnf to set global options,
# mysql-data-dir/my.cnf to set server-specific options
# (@localstatedir@ for this installation) or to
# ~/.my.cnf to set user-specific options.
#
# On Windows you should keep this file in the installation directory 
# of your server (e.g. C:/Program Files/MySQL/MySQL Server X.Y). To
# make sure the server reads the config file use the startup option 
# "–defaults-file". 
#
# To run run the server from the command line, execute this in a 
# command line shell, e.g.
# mysqld –defaults-file="C:/Program Files/MySQL/MySQL Server X.Y/my.ini"
#
# To install the server as a Windows service manually, execute this in a 
# command line shell, e.g.
# mysqld –install MySQLXY –defaults-file="C:/Program Files/MySQL/MySQL Server X.Y/my.ini"
#
# And then execute this in a command line shell to start the server, e.g.
# net start MySQLXY
#
#
# Guildlines for editing this file
# ———————————-
#
# In this file, you can use all long options that the program supports.
# If you want to know the options a program supports, start the program
# with the "–help" option.
#
# More detailed information about the individual options can also be
# found in the manual.
#
#
# CLIENT SECTION
# ———————————-
#
# The following options will be read by MySQL client applications.
# Note that only client applications shipped by MySQL are guaranteed
# to read this section. If you want your own MySQL client program to
# honor these values, you need to specify it as an option during the
# MySQL client library initialization.
#
[client]

port=3306

[mysql]

default-character-set=utf8

# SERVER SECTION
# ———————————-
#
# The following options will be read by the MySQL Server. Make sure that
# you have installed the server correctly (see above) so it reads this 
# file.
#
[mysqld]
skip-name-resolve

# The tcp/IP Port the MySQL Server will listen on
port=3306

#Path to installation directory. All paths are usually resolved relative to this.
basedir="C:/Program Files/MySQL/MySQL Server 5.1/"

#Path to the database root
datadir="D:/Programs/MYSQL/data"

# The default character set that will be used when a new schema or table is
# created and no character set is defined
default-character-set=utf8

# The default storage engine that will be used when create new tables when
default-storage-engine=INNODB

# Replication Master Server (default)
# binary logging is required for replication
log-bin=mysql-bin

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