You can always burn the old bootloader into the Nano with the new bootloader; it will more than likely proof that it's not bootloader related.
Originals or clones. Clones only follow the original's design but can differ; e.g. the power circuit of one clone can be different from another clone.
How many LEDs? How are they powered?
Your topic has been moved to a more suitable location on the forum. Installation and Troubleshooting is not for problems with (nor for advice on) your project 
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