I have the same issue. When checks post they are posting negative transactions. Incoming wires are also often posting negative. Sorry, but it seems this thread seem to brush off customer concerns. The rationale offered is not a likely cause:

-Usually, this happens if you have a large credit card refund that exceeds your new credit card sales on a particular day. 

-Someone entered an incorrect ending balance at the start of the reconciliation.

-misclassification of account.

If this is due to file corruption then I need higher level support to rectify this please. I don't know what it is but I need help in fixing this. I have spoken to customer care but the issue has not been resolved. I am the accountant.