I used "change assumptions" in Lifetime Planner:
"Investments" -> edit, select my 401k entry, in Tab #2 "add" a "new" contribution to my 401k. Define $6000 annually no other increases and no Company match.
See attached screen shots for the"before" vs "after" effect in my Plan Summary. It doesn't look right to me .... the Company contributions "after" the catchup actually increased (see attached.) And, I cannot tell how Quicken treated my catchups further down in the Summary as shown in "Tom contribs" (attached).
I'm trying to duplicate your "before" numbers. I've got the salary ($163,524) and employer contribution ($9,811) to match your "before" pictures, but the Total Tax-deferred is only $29,434. That's about $12,000 short of your $41,085 amount.
Is there some other tax deferred contribution in your plan? If so, I would temporarily exclude that so you can see the impact for the 401(k) alone. You can also exclude the catchup contribution to see its impact as well.
There does appear to be an issue with the employer contribution percentage being applied to all the 401(k) contributions in the plan. I typically adjust the employer contribution percentage to get the right employer contribution amount.