I just noticed that a huge error log is created, 2 mb in size, here is a snippet:
[09-Jul-2013 19:34:46 UTC] WordPress database error MySQL server has gone away for query INSERT INTO
wp_options(
option_name,
option_value,
autoload) VALUES ('rewrite_rules', 'a:19585:{s:48:\"(0-9/1349)/(?:feed/)?(feed|rdf|rss|rss2|atom)/?$\";s:52:\"index.php?category_name=$matches[1]&feed=$matches[2]\";s:31:\"(0-9/1349)/page/?([0-9]{1,})/?$\";s:53:\"index.php?category_name=$matches[1]&paged=$matches[2]\";s:13:\"(0-9/1349)/?$\";s:35:\"index.php?category_name=$matches[1]\";s:47:\"(0-9/311)/(?:feed/)?(feed|rdf|rss|rss2|atom)/?$\";s:52:\"index.php?category_name=$matches[1]&feed=$matches[2]\";s:30:\"(0-9/311)/page/?([0-9]{1,})/?$\";s:53:\"index.php?category_name=$matches[1]&paged=$matches[2]\";s:12:\"(0-9/311)/?$\";s:35:\"index.php?category_name=$matches[1]\";s:43:\"(0-9)/(?:feed/)?(feed|rdf|rss|rss2|atom)/?$\";s:52:\"index.php?category_name=$matches[1]&feed=$matches[2]\";s:26:\"(0-9)/page/?([0-9]{1,})/?$\
It goes on and on for all categories.
Anyone have any ideas?