I think you need to use some str conversions in MySQL before inserting. Or to prepare the data in the proper format, before making the query to MySQL.
The microseconds format is also wrong. MySQL documentation clearly states this:
A DATETIME or TIMESTAMP value can include a trailing fractional seconds part in up to microseconds (6 digits) precision.
UPDATE: on my localhost I've got the same version of MySQL, and it works.
Tryed to execute conversion
select str_to_date("2011-03-13 02:53:50.000000", "%Y-%m-%d %H:%i:%s.%f") as `t`
and gotten:
+----------------------------+
| t |
+----------------------------+
| 2011-03-13 02:53:50.000000 |
+----------------------------+
1 row in set (0.00 sec)
Here's the SQLFiddle, that confirms the thing on other version of MySQL.
I run out of ideas, I think the issue is connected to the "local glitch" in Table structure or specific version of MySQL+OS.