San Bernardino does require a license to rent a property in their city limits.
(Click on the link for the application). The fee is $60 and includes the zoning verification (normally an extra $37/$39).
There is an inspection that needs to be performed by code enforcement that is $100 every year- but if you pass the inspection the first time you will be exempt the next two years (see this link: http://www.ci.san-bernardino.ca.us/depts/community_developme ).
Because you have received a violation there may be a penalty besides the violation to bring you in compliance.
It is very unlikely that they will charge you the maximum of $1000 a day, it is more likely that it will be around $100/$150 a day and since this is a new violation for you, they may waive or reduce the fees but you want to take care of the violation as soon as possible. (I have found that the city has always been very helpful and courteous in my dealings with them, so don't be too anxious).
Many cities have this requirement to help prevent blight due to unmaintained properties. I have even heard of some cities requiring 'permits' for vacant properties- such as bank repos for the same reason.
If you need any help with your property or if you have any more questions, I live in the area and would be happy to help you.
Best of luck,
Like most cities, they are currently understaffed due to budget cuts and can be a bit behind in their inspections and focus mainly on issues/properties on which they have received citizen complaints (sometimes on the rentals it can be because of the tenants issues- i.e. w/ their neighbors or other government departments, and not the condition of the property that causes the city to investigate).
Have a great day,