Sorry to necro, but I had seemed to be having a similar problem.
I'd selected the commander deck type and had built a commander deck. (99 cards in sideboard, 1 commander in sideboard)
Each time I loaded the deck into the deck editor, I received the following message:
"Errors while loading deck
Found problems with deck:
Layout mismatch: Expected 99 cards, but got 98 in layout MAIN"
Trying to create a commander match with that deck, will result in the same error message.
I can fix this problem by going to the source file of the saved deck, copying the card name list, selecting all contents (ctrl + a), and then pasting only the card name list. Reloading the deck after doing that makes the above error message disappear.
If my humble reasoning is to be trusted, the bottom portion of the file ("LAYOUT MAIN:(1,7)(CMC,false,50)|([MPS:16],[MH1:243], ... ") might have somehow stopped synchronizing with the card name list, which was still updated. That could be the result of a bug, maybe with adding or with deleting a card.
EDIT: upon further investigation the error message started appearing after I set the name of the deck, so that's probably where you want to look first.
EDIT 2: it still won't let me create a game with that deck, with the same "deck type game type" message. how strange! any ideas for help?