I believe the county is right.
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An individual renting property is not conducting business, but you have set this up as a business and must register with the state as a business. You should not be putting the rent into your personal account because you are defeating the purpose of the LLC. If someone sues you they can go after you personally. The IRS would also penalize you if you are audited and you are reporting the income to the LLC but using it personally without a distribution from the LLC.
I'm not sure what "short-term" license you received and if it was issued by the state or county, but the Department of Business & Professional Regulations also requires a short-term license and I would think you would have to prove your registration in Florida to obtain.
Also, if you would need to file suit against anyone, you cannot do so without being registered in the state.
The amount of the fees are nominal compared to the problems you could encounter. The fees are $125.
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