Presumably the result of the formula isn't exactly zero, but something like -0.0001 which is less than zero. Normally this displays as 0.00, but I can imagine that with conditional formatting used this will display negative.
If such a cell is, say, d10, make another cell with the formula =d10 and the standard format with 9 decimals to see the exact value.
And, for advice, post the conditional formula you use and that you would want to display 0.00, together with the exact value, if you can't work it out yourself.
It's just a little big vague now, not only for you, but for us here also.
I have a spreadsheet where one column displays the result of a formula. For some reason, partway down this colum, Excel is displaying the zeros as -0.00 instead of just 0.00. I cannot work out why, or how to change this. Zeros display as 0.00 towards the top of the column. I am running Excel 97 on Windows XP. Does anyone have any idea as to how I can sort this out? It is messing up my conditional formatting as Excel considers -0 to be less than 0, and therefore ignores my formatting.