There are several reasons for that difference:
1. Be sure you use the same data for backtesting in both programs;
2. Be sure that the instrument settings are correct (digits, spread, swaps...);
3. If the above conditions are met, the indicators have to show the same values in both programs. If there are differences, you have to check the formulas used;
4. The strategy logic has to be accurately programmed in MT4;
5. FSB uses advanced methods for evaluating the signal conditions. You have to program the same formulas in your expert. You can see the FSB evaluation criteria source codes here: Indicator.cs. These formulas take into account also and the statistical error - Sigma during calculations with "double" numbers.
6. FSB uses various methods for bar interpolations ("Pessimistic" is the default one.) but no one knows how MT4 interpolates the bars.
7. When correct interpolation is not possible, FSB reports "ambiguous bars". Here also MT4 behaves like a black box.
8. FSB protects the user by setting "Use previous bar value" parameter properly for the indicators depending on the environment. You also have to take care about this in your expert.

Actually FSB is here to make faster and more reliable backtest than MT. If you have questions about a specific signal or case, please post as much info as you can gather in order to analyse it.