In the Editor, using the Replace All feature causes the cursor to lose place in the file script. In a search of multiple occurrences string, the cursor will jump to the last occurrence of the searched string.
In the Editor, open the Replace Text dialog and specify whether you want the Origin to be "From Cursor" or "Entire Scope". After running Search & Replace, use the <Ctrl> + <Home> keys together to make the Editor scroll back to your chosen start point.
Use the Quest ScriptRunner (QSR) [free utility which comes with Toad]. This make Search & Replace work exactly as it did pre-Toad 9.0. Use the External Tools button to launch it straight from Toad. The qsr.exe is located in the Toad installation folder. More related information is available at SOL17093 - Script runner documentation.
Waiting for fix in a future version of Toad for Oracle.