My goals are to get a flip going within 3 months and to start building a rental property portfolio with quality management companies handling the day to day operations of them.

Operating Expenses $32,099 !

I'd think they would operate there.

Improving the comfort and efficiency of the building is part of the deal.That said, the bigger players in our area are not quite there yet - most still seem to operate under the mode of "unload utilities on tenants" to improve the bottom line.  

I don't think it matters whether the unit is occupied from a tax point of view so long as you are operating it as a business endeavor (i.e., you're not living in it also).

Commercial tenants can do repairs and improvements, because such can be filed and accounted for in their business operations. 

Diagnostic fistuloscopy under irrigation is followed by an operative phase of fulguration of the fistula tract, closure of the internal opening and suture reinforcement with cyanoacrylate.

That's because they don't operate using the same business methods.  

They should of deducted the leasing fee from the rent and then showed you had a remaining balance with them.They may be operating on a different property management software system and have to do things differently.You need to have a good understanding of your management agreement agreement with the management company. 

You need to know what these are for your local area, ask a realtor or your title company, to be able to identify who owns the property.You might call/visit the local government building or planning department to find out two things; 1) Who owns that parcel and 2) what covenants/operating and use agreements, if any, are in place that control the use and maintenance of the property.