Hi,
generally when we execute sm35, the entires get passed and all the line items in your two Gls (In & Out) gets cleared. Now what you need to check is that your manual recon FF67 that you run is capable of handling all sort of transactions. For general payment done and payment received, it can take care of it on the basis of various interpretations you configure. However certain transactions like Chq Issued but returned or Chq deposited but returned or any Service tax entries or any errorneous entries made by the bank but subseuently reversed, these may have to be manually processed as system will not find any interpretations of it. In fact even in SM35, when it encounters such issue it actually opens you the F-03 screen to let you identify the type of transaction and key in the appropriate GL manually. Hence F-03 may be required even if you are using SM35.
best regds
Subha