Hi,
Those formulas are both read from corresponding template file. In fact it is strange to us that the formula in your given xls is "=Sheet1!$A$2". We don't know how did you create this XLS file, at our end when we save the XLSX as XLS by excel2007, in the saved XLS file the formula was "=$A$2"(same with the formula in XLSX file), not "=Sheet1!$A$2". Anyways, because MS Excel does not allow reference to other worksheet than the sheet where the format condition is in, so "=$A$2" is always equals to "=Sheet1!$A$2" for the conditional formattings in Sheet1.
Thanks for quick response.