Investment account transfers??

I have two investment accounts where I enter share transactions and dividends received and then the funds are transferred to cash accounts.

In the first account all is well and after entering, there is a zero balance. In the second account, the funds are transferred but then is showing a cash minus in the investment account?

I am not entering any franking credits in the first account as that is managed for the super fund but I want to keep track of the bank account.

The second one has everything entered and that is the only difference between the two accounts if that makes sense? What am I doing wrong? Last financial year was my first for being involved with shares and this problem only started at the beginning of the financial year as I had a few transactions the previous year and that didn't happen.

Thanks, June Daley