boot_serial: Fix issue with queued commands

Fixes an issue whereby multiple commands are received and some
are still being processed. This generally arises when a response
takes a long time (e.g. when image decryption is required),
duplicate commands will now send multiple responses but avoids
the bug of future commands being sent to which previous responses
are received.

Signed-off-by: Jamie McCrae <jamie.mccrae@nordicsemi.no>