I checked the box for "Reverse sign of difference for Expenses, Liabilities, and Equities", but this doesn't seem to be working. Why is this and how can I fix this so that the variances are correct?
The "Reverse sign of difference for expense, liabilities, and equities" setting will only reverse the sign of the difference for Expense, Liability, Current Liability, Long Term Liability, and Equity account types in the General Ledger Structure. If an account is not one of those account types, the sign of the difference value will not be reversed.
If the accounts in the report are not Expense, Liability or Equity accounts, one option you might consider would be to use a Custom Calculation for accounts where the sign should be reversed. In the calculation you would then put a negative sign in front of the account to reverse the sign. For example, let's say you wanted to flip a sign on the Report for an account, Interest Expense. To do this, you would delete the line that is currently on the Report for Interest Expense and then pull in a custom calculation with a formula set to -1*Interest Expense.