From: Vermont, USA
Ok, I just took a look at your save with your attack on Baltimore.
I noticed that you are playing with Corps Sub-Commanders ON but most of your CSC slots are unfilled. Your Union opponent, on the other hand, has a fully fleshed out CSC structure setup. This alone is a HUGE disadvantage for you.
If you play with CSCs on, you have to build corps and fill out your sub-commander slots or your opponent will be getting more modifiers than you in every battle.
Your army was also not exactly very large in comparison with the Union army defending Baltimore.
Your Committed forces (less than they might have been due to lack of CSCs) were 7x Infantry, 8x Artillery, 6x Cavalry. On the other side, the Union commmitted 26x Infantry, 13x Artillery, 1x Cavalry, 4x Heavy Artillery. And the Union was defending a Level 2 Fort! So you were attacking into fortifications while outnumbered more than 3:1 in Infantry and 2:1 in Artillery. In addition, your commanders were overloaded (too few CSCs) and thus many of your brigades did not get all the leadership bonuses they should have, while your enemy's forces were all well organized and well lead.
In addition, some of the Union forces were not detected, so they received surprised bonuses as well. I can understand missing a few, but even some of the Heavy Artillery were undetected. There's no reason that should be if you were good about scouting (which you should always do before committing to a major battle). I saw that you committed your cavalry to the battle, it might have been more helpful to actually have them use that movement to scout the enemy some more to avoid those surprise bonuses.
Looking at the combat report, I see scouting by the Union cavalry every turn. In the last two turns I saw NO reported scouting by CSA cavalry forces. You can't win the war without scouting your enemy before battle, period.
Consider a historical assault by a disorganized CSA army on heavy fortifications defended by more Union soldiers than the CSA soldiers attacking them, with the full extent of the Union fortifications and reserves unknown to the CSA commander and the Union army being well organized and fully prepared. It would have been a slaughter and in the game it ended up that way as well.
I would strongly advise you to re-read the CSC rules and play with them off until you feel comfortable with them, as right now they're hurting you a lot more than they're helping you. Also, scout, scout, scout!
Hope that helps explain your results and why the game is working fine. I'm guessing if you lost Vicksburg in the reverse, it was probably also a lack of CSC organization combined with lack of scouting that pushed things over the edge, but I'd need to see a save of that turn to confirm.