I’m using XAMPP on Windows and had the same problem.
I thought it was the timeout variable but it was max_allowed_packet.
This has fixed it:
# note the change was made at this section
[mysqld]
port= 3306
socket= "/xampp/mysql/mysql.sock"
basedir="/xampp/mysql"
tmpdir="/xampp/tmp"
datadir="/xampp/mysql/data"
skip-locking
key_buffer = 16M
# it was 1M by default
max_allowed_packet = 2M
table_cache = 64
sort_buffer_size = 512K
net_buffer_length = 8K
read_buffer_size = 256K
read_rnd_buffer_size = 512K
myisam_sort_buffer_size = 8M
This configuration file is located at «XAMPP install directory, this is C:\XAMPP by default»\mysql\bin\my.ini.