Check your custom Barracks unit. What does it have its "Stats -Life Starting Amount" set to, compared to its maximum life?
Edit: Durr, stupid me. Completely mis-read the problem.
Does your custom Barracks have the "Build in Progress" ability? I'd also check the Actor Events and compare them against what the normal Barracks has. If all else fails, just duplicate the vanilla Barracks and change which unit its Actor Events point to.
Check your custom Barracks unit. What does it have its "Stats -Life Starting Amount" set to, compared to its maximum life?
Edit: Durr, stupid me. Completely mis-read the problem.
Does your custom Barracks have the "Build in Progress" ability? I'd also check the Actor Events and compare them against what the normal Barracks has. If all else fails, just duplicate the vanilla Barracks and change which unit its Actor Events point to.