First of all I want to say sorry for kicking the dead horse and my English...
But since this is the first result when googling for something like "flash drive showsing as two drives" I decided to post the answer...
This is indeed caused by flash drive's firmware, but it's not very difficult to fix it anyway.
This is also the fix for those fake usb flash drives (drives with fake capacity, "256GB" sticks with only 1GB chips in them
Find your device vendor and ID's either by looking on controller chip or using software like ChipGenius (in my case it was Alcor SC908AN)
What you need is MPTool (Mass Production Tool) for your specific controller. Sometimes they are vendor generic, sometimes device specific (it was the second case for me). So google "MPTool ", and you are likely to find some links to manufacturer's download page.
USE MPTools WITH CAUTION! You CAN render the drive useless, so be sure to backup the firmware if it's possible with your tool or be prepared to throw it away if something goes wrong.
Format your drive after firmware is reflashed
I am not responsible in any way for any damage caused by this steps. Hope this guide helps