There are a few reasons for this difference which we will gladly and exhaustively review below:
1) When you first setup your account, there is a 7-10 business day verification process. Your early/initial charges may have a general delay. No need to worry. Once your account has been verified, the flow of deposits will be much more regular.
2) Stripe may need further information from you. Log into your Stripe.com account directly to check for any requests for further information that may have put a hold on funds.
3) Stripe batches at 8pm EST/12am UTC. Pay for any online orders processed after this time will roll into transfers for the next business day. When checking the accuracy of your transfers, make sure to include previous day transactions after the previous day's batch time.
4) Some of your transactions are cash. Make sure you don't expect deposits from orders that were paid directly to you in cash.
5) You must factor in the processing cost. Each transaction is charged 2.9% + 30 cent for processing. This will be taken at the time of the transaction. For example -- on a $100 order, you will receive $96.80.
6) Note that transactions fees on cards are taken before funds are transferred into your account. Do not be alarmed by the transfer amounts being slightly less than what you see in your order reports.
7) Transactions are based on business days. You will not see deposits on the weekend. Weekend transactions will be rolled into future business days.
8) In the US, the default transfer schedule for restaurants is 7 business days for your first transfer and then a rolling 2 business day basis. Should you wish to alter that schedule, you can make transfers less frequent (weekly or monthly) within your Account Settings. You cannot, however, make transfers more frequent due to bank regulations.
9) For further clarification see the following two articles:
10) If for some reason the answer to your question is not contained above, you should contact Stripe.com directly at email@example.com.