After my first tenant turnover I added ceramic tile in the living room and hallway, painted the whole house, and replaced all of the windows in the house.

The more you study and research your niche, the higher your confidence will grow in your purchases and the uncertainty will be out the window!

I send over my handyman and he discovers that a window unit(non authorized) leaked condensation back into the sub floor and has caused about 500-600SF of sub floor and flooring damage. 

My parents did a quick walk-around and saw that all windows need to be replaced, driveway re-paved, etc.

I have added several upgrades being new windows, roof, carpet, etc...I know have (potentially) $120,00 in equity.

Now go back and create a scope of work that will get you to the target, and of course you are looking at things that increase value like - kitchens, bathrooms, mechanicals, roof, windows (these are your value earners). 

However this takes a good chunk of the Cash Flow during the winter months.The building came with double pane vinyl windows.

Had window broken 3 times in the span of about 4 weeks at this property too.

@Solomon MorrisDoesn't sound like the control board would do squat for that issue.Here are your options:1 - Window Unit upstairs (on the AC side) - does same issue occur in winter?

The window I assume leaks in the winter.