I have the same question.

when you look at the budget vs actual, it doesn’t take into account the amount’s transferred from operating to reserve and gives an inaccurate bottom line. 
i have the same issue with a LOC payment. It decreases the liability and expenses the interest amount of the payment but on the budget, it doesn’t take the entire amount into consideration when using budget vs actual and makes it look like we’ve spent less money than we have.

I dont think QB is the best software for an HOA and am looking elsewhere.