If you have an active root...over time it will grow back in there unless you excavate, cut and remove. 

We deliver our properties free of both (noted as such in the lease) and then contractually make the tenant liable for prevention/termination. 

I would say on a rental property that's unrealistic, if it really is an issue on a property, better to address the root cause.

In other words, I already have a checking and savings with BoA, but I would create a 2nd savings account (within my regular account) and put all the rental properties last months and security into that account (combined).Is this the correct way to prevent co-mingling of funds, or what would you recommend?

I guess I can't wrap my head around the fact that anyone can make an argument as to how the doors and windows being left open was not the root cause of this issue.

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So can I calculate my cash on cash return like below $40K(appreciation)/($42k(Down payment)+(2.1K(Monthly payment for Mortgage+HOA)*36)) = 40/(42+75.6)= 34% so the annual cash on cash return is about 1.34 to find the cubit root.

Can anyone recommend good companies to root cause  and implement solution to fix this issue?

Generally no because the root system is still in place.

What specifically did you expect them to do to prevent them?