The beg balance changes when you transfer funds between bank accts without using a clearing account.  You reconcile one acct and the beginning balance changes for he other. 
You should only transfer funds using 1-1 or 1-2 options, transfer funds. This will create two transactions so that you can clear them separately for each bank acct 

Review all the transfers to find the ones causing the issue. Unclear them. Void them. Recreate them the correct way. Clear the one for the account that was already reconciled. Then reconcile the other account. 

Thanks for commenting the issue is that when the cash account was set up, the beginning balance was not entered.  When I reconciled the first time, the account was already set up and I could not enter the beginning balance in that field on the account set up.  To reconcile, I entered the beginning balance as a deposit debiting the cash account and crediting an account that someone else in our company titled as a "Startup" account.  That "startup" account has a negative balance which is incorrect.  Is there any way that someone can enter the beginning balance on the general ledger account field in 1-7?

These are the procedures you should have followed for starting balances.

Post a JE for your trial balances.

Then......................

About clearing outstanding bank transactions

Before entering outstanding transactions, you may need to clear existing transactions. Such transactions are usually the result of entering the beginning and period balances.

For the first time reconciliation for a new company, work on only one account at a time.

For each bank account, enter the open bank transactions that are part of the startup ledger balances. If you have written checks or made deposits that are not included in the startup ledger balances, do not enter them at this time. Wait until you have finished entering all start up data.

Because the effect of the outstanding bank transactions are already encompassed by the ledger account balances set up earlier, post the transactions to a clearing account in the period prior to the current period. Suppose you are setting up during period 7. Post each open transaction to period 6. Then post the journal transaction to the end of period 6.

Working on the outstanding items for one bank account at a time helps prevent startup errors.

Entering outstanding checks or bank charges

When working with a bank charge, you can type Bank Charge in the Check# box on the 1-1 Checks/Bank Charges window. You can also type it as BCmm/dd/yyyy (where mm/dd/yyyy is the actual date of the bank charge). Sage 100 Contractor saves the information and displays the resulting transaction the 1-5 Bank Reconciliation window with Bank Charge in the transaction number (Trans#) column in the checks area.

Caution! Do not enter a vendor number. It would otherwise affect the 1099 balances. The 1099 balances are set up later.

To enter outstanding checks or bank charges:

1. Open 1-1 Checks/Bank Charges.
   1. Account#:  Checking Account #____________
   2. Check# box, enter the check number.

Date box, enter the date of the check.

1. 1. Description: Outstanding from (prior software)
   2. In the Status list, click 1-Open.

1. In the grid:
2. In the Description cell, accept the default description from above

• In the Account cell, enter the clearing account number #_______________

1. 1. In the Debit Amount cell, enter the individual check amount.
   2. Save.
   3. Repeat steps 3–9 until you have entered all outstanding checks for the account.

To enter outstanding deposits

1. Open 1-2 Deposits
   1. Account #: Checking Account # ____________
   2. Deposit #   (I prefer to just let Sage start at #1, and then continue sequentially so that they will be in the right order when you do the bank rec and sort by transaction # which is the best choice for checks, so then they are both in the right order)
   3. Date
   4. Description:  outstanding deposit

1. Down in the grid
2. Description ; accept default

• Account: Clearing Account #___________

1. Credit amount: total of deposit

1. 1. In the status select 1-Open

To Enter the journal transaction to zero out the clearing account.

1. Run the 2-4-31 General Ledger Report Landscape
   1. Clearing Account #_____________
   2. Make note of the balance

1. If it is a positive balance (typically) then you will credit this account in the JE below
2. If it is a negative balance then you will debit this account in the JE below

1. Open 1-3 Journal transactions
   1. Transaction #   JE-offset
   2. Date:  End of month before go live date
   3. Description:  outstanding offset
   4. Banking Category: Adjustment
   5. * Status = should be 2-cleared (you are putting the funds back into checking to make the starting balance correct, so that you can clear the outstanding checks in your first bank rec)
   6. No payee info needed

1. In the Grid
2. Row 1
   1. Debit or Credit the clearing account as noted above

• Row 2
  1. Debit or credit the checking account

1. Verify the clearing account is zero by repeating step 3 above
2. Open the 1-5 bank rec screen and verify the starting balance for the checking account is correct.
3. Then proceed to the next bank account. (Note:  You can use the same clearing account to enter the balances for each bank account as long as it nets back to zero each time).

OK I am seeing your image now.  You entered the startup amount to cash and to startup contract receivables, which means they have NOT paid you yet.  Is that what you intended?  Startup AR entries are for unpaid invoices.  You then enter an actual invoice in AR for each job and invoice but down in the grid you code it to the STARTUP AR account (not the default which is income because the income was recorded when you booked the original invoice in your prior software). 

No you cannot enter a beginning balance on the account (like QB does, which then creates a credit to a fake account called beginning balances).  Instead you should be posting a complete Journal entry for ALL your account balances listed on your Trial Balance.