The magic item in question is a sword that makes the wielder larger, stronger and more aggressive.

Properties:

• Bonus - Melee Weapon Attacks = 1
• Bonus - Intimidation = +1
• Bonus - Persuasion = -1
• Bonus - Deception = -1
• Bonus - Athletics = +1

For some reason, it's applying a +1 to every skill, then applying the bonuses listed above.  So every skill jumps up by 1, except the skills listed above, which stay the same or go up by 2, depending on the +1 or -1 applied.

Any ideas what I'm doing wrong?

Somewhere in there you must have (or have had) the following:

If you did have it and removed it already, then please see the General Homebrew FAQ #s 6 & 6-B: (https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/131411-a-homebrewers-how-to-faq).

Thank you.