Consider the two following configurations, the only difference being the number of tanks on the side-boosters:
Clearly, the second configuration (with more fuel) should have more delta-V. Yet, it doesn't - by a 600m/s margin. The fuel lines are correctly configured (flowing into the center tank) - though an uneducated guess would be that they could be what's tripping up the dV calculation.
Craft file (note - contains a lot of other stuff as well): https://pastebin.com/A5czZYD4