SQL ran in editor is not being saved in SQL Recall's history tab as expected.
Verify settings in View | Toad Options | Editor | Code Assist -- SQL Recall.
Run query in editor with F9. If it is not run with F9 Execute Statement, it will not be saved as history.
Rename the SavedSQL.dat file in C:\Documents and Settings\<personal folder>\Application Data\Quest Software\Toad for Oracle\<version>\User Files.
Keep in mind that doing so will force a new blank SavedSQL file to be created, and there will be no access to previous history, and Named/Personal SQL.
It is not advisable to manually edit the SavedSQL.dat files.