Okay, I've had a look at the character that SpectreMarkIV provided, and I've diagnosed the problem. It's a weird corner-case bug in how Weapon Finesse was implemented by Hero Lab itself -- the World is Square rules only allowed for the highly specific set of circumstances that trigger the bug to occur.
The problem happens when all of the following are true:
1) You have Weapon Finesse
2) Your STR modifier is higher than your DEX modifier
3) You have a finessable weapon equipped
4) You have a shield equipped
When these conditions are satisfied, Hero Lab applies Weapon Finesse's clause about the shield's armor check penalty to finesse weapons even though the PC isn't actually using Weapon Finesse. The PC's attack bonuses are all calculated using the STR modifier, because it's the higher of the two, but the shield penalty goes through anyway. Effectively, the PC gains no benefit from the feat, but still takes its penalty.
I have attached a portfolio demonstrating the problem without the WiS rules getting involved.
SpectreMarkIV, your PC has Weapon Finesse (even though it doesn't look like it!) because the WiS rules give that feat for free to everyone, and then hide it in the list of feats. Your Strength is 18 (+4), your DEX is 16 (+3), you have a shield, and you have Weapon Finesse thanks to the WiS rules. So you get hit by the bug. If you disable the WiS rules, suddenly your PC doesn't have Weapon Finesse any more, and so the bug goes away.
In the ordinary course of things, this is unlikely ever to happen. No sane player would choose to take the Weapon Finesse feat when their STR mod is already higher than their DEX mod. No sane GM would give Weapon Finesse to a monster that could not benefit from it. And so the bug escaped notice.
One could argue that interpreting the rules strictly as written means that this behavior is correct. The feat says: "If you carry a shield, its armor check penalty applies to your attack rolls." Full stop. If you have the feat, you take that penalty, no if's, and's or but's.
A particularly sadistic rules lawyer could even make a plausible case that since the feat says "carry" a shield rather than "wield" or "use" a shield, you take that penalty any time you have a shield in your immediate personal possession, including strapped to your backpack or stuck in a bag of holding. And because it does not specify "finesse weapons," but instead says "your attack rolls" it should logically apply to every attack roll you ever make: with spells, with weapons light OR heavy, with your fist. Everything.
Clearly, that is NOT the intended behavior in the case of the WiS rules as written by Michael Iantorno. They eliminate Weapon Finesse entirely, allow the PC to choose whether to use their STR or DEX mod, and do not say anything at all about shields or armor check penalties. I only wound up giving Weapon Finesse to everyone because that was the easiest way to implement the change. I figured it would just pick the higher of the two modifiers with finessable weapons, and that would be that. After all, why would anyone choose the lower modifier?
I am uncertain what to do at this point. Question for Aaron or Mathias: would it be better to file a bug with Wolflair to get a fix for this extremely obscure bug, or just compensate within the WiS rules?
In the meantime, SpectreMarkIV, I suggest using adjustments to give yourself a +2 bonus on your unarmed strike and your dagger until this gets sorted out one way or the other.