I have found the real problem, changing the title and the description
accordingly.

** Summary changed:

- "Mark All Upgrades" removes all previous markings
+ "Mark All Upgrades" clears packages marked for removal

** Description changed:

- Synaptic 0.63.1, Ubuntu Maverick
+ Synaptic 0.75.1ubuntu1, Ubuntu Natty
  
- 1. Mark something for complete removal. (For the purposes of reproducing this 
bug, you may want to install something you don't care about, so you can try 
uninstalling it. In this case, I was uninstalling 3dchess, gnome-chess, 
gnuchess, etc.)
- 2. Decide you also want to install any upgrades, so click "Reload", then 
(when it's finished) "Mark All Upgrades".
+ 1. Mark a package/some packages for removal/complete removal.
+ 2. Click the Mark all upgrades button (You can click Reload before, but that 
doesn't change the behavior, it's the same with or without packages to be 
upgraded).
  
  What should happen:
- * The upgrades are marked.
+ * If there are any upgrades available, they should be marked, otherwise 
nothing should happen
  
  What actually happens:
  * The upgrades are marked. (Today there happened to be none.)
- * The uninstallation you wanted is cleared.
+ * The packages selected for removal you wanted is cleared.

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https://bugs.launchpad.net/bugs/50837

Title:
  "Mark All Upgrades" clears packages marked for removal

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