I think I get it now. Thanks!
社長にプレゼントをいただきました。 = I humbly received a present from the manager.
社長に手伝っていただきました。 = I humbly received some help from the manager.
社長に私たちの気持ちを分かっていただきました = We humbly received an understanding of our feelings from the manager (stupid translation I know, I'm just trying to get my head around it)
私の気持ちを分かっていただいてありがとうございました = Thank you for (giving me) an understanding of my feelings.