Simulation simulation output data different for the same input data

I have a complex Simulink (2010a) model with many subsystem blocks in it (some blocks have feedback inputs). Currently, I am getting different result for the same model when I run the simulation in normal mode vs Accelerator mode. To find out the cause of the different result values I am trying to isolate each subsystem and analyze said subsystem's output signals.

To isolate a subsystem I do the following: say I want to analyze B's output signals.

I connect all of A's outputs to ToWorkspace blocks. I run the simulations so the new variables become initialized. I then disconnect B from A. I then feed in B's inputs using FromWorkspace blocks. The final isolated B subsystem looks like

When I compare the simulation results of B's output between the two layouts( figure 1 and figure 2) I get slightly different values. If the input signals are identical then B's output should be the same regardless of where the input comes from (Subsystem A vs Workspace variables). I tried playing around with the Workspace blocks' decimation and sample time and interpolation settings to no avail. Am I correct in thinking the following? By reading variable from the workspace Simulink generates a different set of differential equations compared to Figure 1. So the difference in the output signals is cause my the numerical difference of solving different differential equations for figure 2 verses figure 1?