やっぱりダメでした。
Connection.Begintranceで落ちます。トランザクションがサポートされていないとの事です。

My.iniの内容はこんな感じなんですけど変ですか？
default-character-set=sjis
datadir=C:/mysql/data
port = 3306
socket = /tmp/mysql.sock
skip-locking
set-variable = key_buffer=16M
set-variable = max_allowed_packet=1M
set-variable = table_cache=64
set-variable = sort_buffer=512K
set-variable = net_buffer_length=8K
set-variable = myisam_sort_buffer_size=8M
log-bin
server-id = 1

# Uncomment the following if you are using Innobase tables
innodb_data_file_path = ibdata1:1000M;ibdata2:500M
innodb_data_home_dir = c:\ibdata
set-variable = innodb_mirrored_log_groups=1
innodb_log_group_home_dir = c:\iblogs
set-variable = innodb_log_files_in_group=3
set-variable = innodb_log_file_size=30M
set-variable = innodb_log_buffer_size=8M
innodb_flush_log_at_trx_commit=1
innodb_log_arch_dir = c:\iblogs
innodb_log_archive=0
set-variable = innodb_buffer_pool_size=60M
set-variable = innodb_additional_mem_pool_size=6M
set-variable = innodb_file_io_threads=4
set-variable = innodb_lock_wait_timeout=50