I think my whole file is corrupted. I went through and found that i had some hidden payments in my bank feed. these were the full amount of the EFT for 3 runs that i had done but did not match to the feed as i had paid them off from the overdraft account instead of the electronic clearing account. I have just gone back into disbursments and paid them all off electronically instead.
Now i am missing the individual payments in my reconcillaiton window and i have no dispursment recorded in transaction journal.
I can also confirm i have different expected balances under the 'find trans' under the accounts tab compared to the reconcilled expected balance.