MySQL query 'going away' on executing INSERT ON DUPLICATE UPDATE statement with a 12524 character blob
This sounds like you have to increase the size of your MySQL Packets

According to the page 99 of "Understanding MySQL Internals" (ISBN 0-596-00957-7), here are paragraphs 1-3 explaining it:


  MySQL network communication code was
  written under the assumption that
  queries are always reasonably short,
  and therefore can be sent to and
  processed by the server in one chunk,
  which is called a packet in MySQL
  terminology. The server allocates the
  memory for a temporary buffer to store
  the packet, and it requests enough to
  fit it entirely. This architecture
  requires a precaution to avoid having
  the server run out of memory---a cap
  on the size of the packet, which this
  option accomplishes.
  
  The code of interest in relation to
  this option is found in
  sql/net_serv.cc. Take a look at my_net_read(), then follow the call to my_real_read() and pay
  particular attention to
  net_realloc().
  
  This variable also limits the length
  of a result of many string functons.
  See sql/field.cc and
  sql/intem_strfunc.cc for details.


Since MySQL Packets can hold rows of data, larger items in the packet can cause a lot of packets to filter in-and-out to prevent whole chunks of related data from splitting during processing. This can be a silent killer of DB connections for no apparent reason. If fact, I wrote a post about how this can affect certain mysqldumps.

Try increasing the max_allowed_packet (256M) using the following command:

SET max_allowed_packet = 1024 * 1024 * 256;