Sounds like you didn't implement the Auto Reset hardware properly.
When you load a fresh bootloader it has nothing better to do than sit around waiting for an upload.
Once a sketch has been uploaded the bootloader will only look briefly for an upload after a reset and will then turn control over to your sketch.
To upload without a working Auto Reset you have to use a manual reset. Hold down the Reset button (if you didn't include that either, short the Reset pin to Ground) until you see the "Binary sketch size:" message on upload. This should give the bootloader control at just the right time to notice the upload attempt.