Excel for Mac 2011 calculation results equaling zero are formatting as a positive zero value instead of zero suppressed zero?
Unfortunately, without a sample spreadsheet, we need to start with a debugging exercise-- is this a formatting problem or a formula problem?  Here's one way to approach the debugging. 


Set up an "indicator" or verification cell formula to verify:  is the running balance cell equal to Zero (TRUE or FALSE)? Is it greater than Zero (again, TRUE or FALSE)?    If you can verify that the value, displayed as "0.00" is in fact greater than zero -- you can trace why you have a formula leaving you with a very small value and not zero.  (You may have a very small rounding error, e.g. add 1/3 and subtract 0.33 -- balance is non-zero.)
If the cell check confirms the  cell is equal to Zero, yet is being formatted incorrectly:  tackle the in-cell formatting followed by the conditional formatting (if any). 
First, check carefully your custom number-formatting string.  Reset your formatting string to a "known good" string -- the generic ones provided in the Format:Numbers box.
Finally, check conditional formatting by breaking down to one (1) condition at a time to isolate the condition which isn't working.