If you don't have any debt on budget (CC debt for example) - then it should be equal.
Debt is what throws the numbers off.

For example:
you have 1000€ in your accounts, have 1000€ budgeted (Total available) and no CC - or otherwise - debt (TBB is always zero because YNAB philosophy ;) ).
Total Available = Account Balance.
Now you use your CC to buy 100€ stuff, the "total available" doesn't change, your account balance doesn't change, everything still fine (except you incurred a debt that is not yet reflected. But the numbers are still fine).
The credit card gets charged - debt incurred. Now your "Total Available" is still 1000€, because you have not yet paid anything, but your account balance is only 900€ - because you owe the CC company 100€.
If you repay them - the "total available" will drop to the 900€ and everything is once again fine.

This doesn't necessarily mean you budgeted more than you can spend, it could also mean you just have budgeted your debt but not yet paid it.

Hope this helps a bit.
And I also hope I haven't completely misread what you meant.