If your Custom Command outputs some text, it's not inserted in the cursor place, it replaced the whole line. Steps to reproduce:

1. Open Edit -> Format -> Send Selection to -> Set Custom Commands
2. Add new command echo "foobar", click Ok
3. Place the cursor in empty line and type some text. For example important text
4. Press Ctrl+1 to perform the created command. Number may differ if it's not your first custom command.

Result: the line has been completely replaced by foobar text.
Expected result: the foobar added after the important text

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