I was having a very similar issue. My external drive is partitioned: time machine partition (HFS) and other partition (FAT). When I attempt to "secure empty trash" (or just regular empty trash) I get a message indicating that I do not have sufficient privileges/permissions, etc. I was able to determine that the files causing the issue were files that I had deleted from the external drive. I unhid all files and discovered that the files I thought I had deleted from the external drive were actually still there (buried in the .Trash folder) and I was unable to delete that folder or the files hidden within.
So, I unmounted the drive and connected it to my PC. From the PC I deleted the ".Trash" (or was it ".Trashes"?) folder. Then unmounted from PC and reconnected to Mac. Now the files are gone and my trash is not bloated with files as it was previously.
I realize this is a 'workaround' that may not be available to you (and everyone), but if you have access to a PC this may solve your issue.
If there is a straightforward way to accomplish this within the Mac OS X environment, please do tell/explain!!
Hope this helps!
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MacBook Pro 12,1 – Yosemite (10.10.3)