Why does investment data throw my checking balance off? Help

I have been a long time user of quicken. I tried to input investment data years ago. Recently I tried to update some of my investment data. I realized that my balance in my checking account was altered by changes in my investment account. Is there a way to isolate and use the portfolio aspect of the program without allowing it to mess with my checking account balances? I am sure that my earlier attempt at inputting investment data may have included account transfers, it would take hours to sift through years of my quicken checkbook data to find the culprit.

Looking for a quick fix.

Thanks