If you print a Check Register, does it show those checks as Cleared? There should be either a "T" or nothing on the right hand side under "Cleared?".
 
Assuming they are not Cleared, are you leaving the "From" date at 00/00/00 on the opening screen where you pick the bank account? Or at least before the date of the oldest check?  
 
I always use 00/00/00 as the beginning date to make sure I'm catching everything. I also go at least one business day past the statement date in case some transactions actually happened the day before we expected them (most often that's CC deposits, especially Amx, which we expect to take 3 days but sometimes only takes 2).
 

Quote from JereC on 10/06/15 at 12:13:10:

 
I think this will work... adjust the "Statement Ending Balance" by that amount. Then you will be at 0, and since the checks were already cleared last month you should be good from here on out.  
 
The only thing I'm not 100% on is that since you'll be saying that the Ending Balance is different, next month the Beginning Balance may be off. However, I think at that time you can correct it by going into AD-B.

The remaining problem is there are two checks that show cleared however they are not cleared yet.  When they do clear eventually I am assuming I will have to adjust the balance again since I can't get them back on the reconciliation,  
 
Jere

Sorry, I realized they would not be on the aging.  However, they will eventually show up on my bank rec to be cleared and they will not be on my DBA rec.  
 
Jere