Tested on

Ubuntu 10.04.4 LTS Desktop - 32 Bit

gedit:
  Installed: 2.30.3-0ubuntu0.1
  Candidate: 2.30.3-0ubuntu0.1
  Version table:
 *** 2.30.3-0ubuntu0.1 0
        500 http://ca.archive.ubuntu.com/ubuntu/ lucid-updates/main Packages
        100 /var/lib/dpkg/status
     2.30.0git20100413-0ubuntu1 0
        500 http://ca.archive.ubuntu.com/ubuntu/ lucid/main Packages

List of active plugins:
gconftool-2 -g /apps/gedit-2/plugins/active-plugins
[modelines,spell,docinfo,filebrowser,time,externaltools]

No output when started in terminal and running the remove trailing spaces tool 
that uses identical sed:
#!/bin/sh

sed 's/[[:blank:]]*$//'

So I guess it's not sed's fault.

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https://bugs.launchpad.net/bugs/995747

Title:
  Gedit: Remove trailing spaces feature removes last line.

Status in “gedit-plugins” package in Ubuntu:
  Confirmed

Bug description:
  Ubuntu 12.04 LTS, 64Bit
  Gedit 3.4.1

  Here's what happend.
  1. Launch gedit.
  2. Create new file type. I am writing PHP file when I noticed it. So I 
created a PHP file.
  3. Put some codes/strings in there. Be sure your last line is a text.
  4. Use Remove trailing spaces feature of gedit.
  5. Observe, the last line will be trimmed.

  
  I expect, only trailing spaces will be removed.
  I found out that the last line was also remove.
  I also use other programming languages and still removes the string.
  Attached is the sample string I made.
  Open it with gedit 3.4.1 and remove trailing spaces.
  The comment should not be removed.

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