First of all welcome to ABM! :-).
There could be multiple reasons why you are seeing mis-match between the CRM accounts that you have selected in CRM and what you see in the 'Discover CRM grid' of ABM -
Reason 1 - You have CRM accounts with no contacts - You selected CRM accounts that doesn't have any contacts associated with it. To see CRM accounts in Marketo discovery, you need to have atleast 1 contact associated with the CRM account.
Reason 2 - You have CRM accounts with same names - ABM de-dupes CRM accounts by account names. To find duplicate accounts, ABM also normalizes the CRM account names by removing unneeded suffixes (any of the following suffixes: Co, Corp, Corporation, Gmbh, Inc, Incorporated, LLC, LLP, LP, Ltd, PA, PC, PLC, PLLC). E.g. ACME and ACME Inc. will be de-duped into 1 ACME.
Reason 3 - Accounts are not synchronized into ABM yet - If Reason 1 and Reason 2 are not true then check in your lead database, if you have contacts from the CRM accounts that are not seen in the ABM discovery. If you don't find contacts which means those accounts are not synchronized yet.
Also when you select CRM accounts in CRM system using custom field, it might take some time reflect that in ABM depending on how fast your CRM data is synced into Marketo.
I will ask our documentation team to document above details. Pl. send me the email directly (firstname.lastname@example.org) for any further questions that you may have on ABM. We want to make sure your journey with ABM is as smooth as possible.
Hope this helps.
MJ (Mahesh Jeswani)
I have seen these issues too. More like bugs when you try to select accounts and you get errors. Our pro serv guy has run them up the flagpole to the dev team.