Quickbooks has held our deposits and payments from invoices. They've also limited the instant deposits on our account. 
The customer service teams don't ever have the same information and I've been told things ranging from our monthly deposit limit is $20k to daily of $288,000; I've also been told that our funds would be available the next business day; then told the next day; then told 1-2 days. We pay a ton of money in processing fees to Quickbooks not to mention have paid an increase in our monthly subscription. If anyone else is experiencing these issues, let us know. We are looking into filing suit agains Quickbooks.