If you haven't done so already, copy/paste this command into Terminal
defaults write com.apple.DiskUtility DUDebugMenuEnabled 1
Then in the Disk Utility Debug menu, select "Show every partition"
I would check the disk for primary partitions and delete them. Then format the whole disk as Mac OS Extended (Journaled). It may be that the 100Mb one is a normally hidden EFI partition, which you should not interfer with.
I also erase any propriatry software from the disk manufacturer, which causes more trouble than it is worth.
But since there have been problems with data loss on some Western Digital disks, check your's isn't one of them. There was a long thread on the subject on ASC.
http://www.macrumors.com/2013/11/26/western-digital-releases-new-hard-drive-soft ware-after-mavericks-data-loss/
https://discussions.apple.com/thread/5475136?tstart=0