@psychadelic: Every time that someone has reported that, it is because of the save template used for sending books to the device. At a guess, you have changed the template to use the series name for the file name. Which means whichever is sent last replaces the first. The default template is something like:
Code:
{author_sort}/{title} - {authors}
You have probably replaced the "{title}" with "{series}" or something like that.
Check what you have in the save template for the driver for your device. There is a default on the "Sending books to devices" page of the preferences, but, is only used if you have not configured the driver.