I balance my checkbook(s) monthly.  each time they balance, I underline the balance and write in the checkbook "balanced".  That way I know the checkbook is balanced to that point.

From what I read, I presume you balance it monthly as well.... since you mention "2 months" (?).  

a) I would go back to the point where you had it balance last, and I would take all the information from that point and recheck it.  I would take a spreadsheet, set it up to do the math (very simple if you are used to spreadsheets), and I would enter the initial balance and all the deposits and all the withdrawals; let the computer do the math, and verify that you did not make a math mistake somewhere along the line. 

b) I will subtract the bank's balance from your balance (or vice versa), to see what the difference is.  Sometimes, that amount will help you identify where to look.

c) Sometimes I would look at the "inverse" of the difference.  for example, if the difference is less than $10, I would take $10 minus the difference, and look at that number - see if it shows up anything.  Or if it is between $10-$100, I would subtract $100 minus the difference, and look at that number.  If this helps to identify your error, then I would think it would be showing a subtraction error somewhere along the line. 

At the end of the day, you might just need to use the bank's balance and start over from now.  I don't like to do this, because, it would be my luck that this would screw up my checkbook worse than ever.  So, personally, I like to track down the error and get my checkbook balanced "the right way".

my 2 cents.