It turns out that if your total income is between 100k and 150k the portion of losses reported on Schedule E changes on a sliding scale from 100% at 100k and 0%...
Alright - I had to set up an excel spreadsheet but I found what was causing the difference (thank you for @macuser_22 for pointing me in the right direction!):W...
Thank you @macuser_22! I added it in the 1099-R/income section, so not in the contribution section. The 50% penalty shows up in the My Account>Tools>View Tax Su...