I've found a small problem in TortoiseMerge using the Find/Replace function.
I've opened a file (TortoiseSVN, Diff), pressed Ctrl-F to open the Find dialog. It automatically fill the "Replace with" with the same word I used last time. I've changed the Search for to whatever I want to replace (see picture merge_replace_1.png). I press the key Delete to clear "Replace with" and then Alt-A to replace all. TortoiseMerge uses the old value of "Replace with" instead of replacing with [nothing] (see picture merge_replace_2.png).
If I instead change the "Replace with" to something new (for example "ant"), the Alt-A works as expected. It also works if I move focus out of the input box (for example pressing Tab) or if I click the Replace all button.
It seems that TortoiseMerge saves the value for "Replace with" in a variable that is only updated on when the input box looses focus or whenever something NEW is written in the input box.