By default, the way you do this is with a level-by-level approach:
Scout 1 (+0/+2/+0) // Ranger 1 (+2/+2/+0) = +2/+2/+0
Scout 2 (+0/+1/+0) // Swashbuckler 1 (+2/+0/+0) = +2/+1/+0 (total: +4/+3/+0)
Scout 3 (+1/+0/+1) // Swashbuckler 2 (+1/+0/=0) = +1/+0/+1 (total: +5/+3/+1)
Scout 4 (+0/+1/+0) // Rogue 1 (+0/+2/+0) = +0/+2/+0 (total: +5/+5/+1)
So neither you nor Heroforge is right.
That said, these rules are dumb. They work out reasonably well for this particular build at this particular level, but there are a lot of combinations where these rules result in extremely poor bonuses for no good reason. The characters that result are inconsistent with the expectations of the system.
A better method, in general but especially with gestalt, is to incorporate Unearthed Arcana’s “fractional BAB/saves” scheme. In this, you round down after adding up your classes, rather than before. It results in a much cleaner, consistent BAB and saving throw progression.
If you use that, the progression becomes this:
Scout 1 (+⅓/+2½/+⅓) // Ranger 1 (+2½/+2½/+⅓) = +2½/+2½/+⅓
Scout 2 (+⅓/+½/+⅓) // Swashbuckler 1 (+2½/+⅓/+⅓) = +2½/+½/+⅓ (total: +5/+3/+⅔)
Scout 3 (+⅓/+½/+⅓) // Swashbuckler 2 (+½/+⅓/+⅓) = +½/+½/+⅓ (total: +5½/+3½/+1)
Scout 4 (+⅓/+½/+⅓) // Rogue 1 (+⅓/+2½/+⅓) = +⅓/+2½/+⅓ (total: +5⅚/+6/+1⅓)
And then round down for a final saving throw progression of +5/+6/+1. Minor improvement to Reflex, which makes sense because you are taking three different classes with good Reflex saves.
I also strongly recommend eliminating the repeated +2 for each time you take a new class that has a given good save (this is not a part of the Unearthed Arcana variant, however). In this case, you would miss out on the +2 from Swashbuckler 1 and Rogue 1, and have a final, rounded-down saving throw base of +3/+4/+1 – very similar to a typical, single-classed character. This way multiclassing doesn’t have weird positive or negative effects on your saving throws, aside from the natural consequences of having good or bad saving throws.