I wouldnt deposit a check at a third party ATM, but at that branch or a bank-owned ATM I have no problem.
It could take a few days to get your full funds (my bank allows the first $100 to be available instantly, but I have a balance...I am not sure if you had negative or a low balance if they would allow that).
I have heard those arguing at the branch though that they deposited a check on Friday via an ATM and why is it not available 'today' (being the day after/Saturday).
The reason for only allowing $100, if anything is that the whole ATM deposit system is honor based. If they didn't limit you, one could find a remote ATM...punch in any amount and then start withdrawing over the next few days.
If you need the money in the account ASAP use the counter or the night depository at the branch.