We're having the same problem but with livestock settlements.  And we're using Quickbooks desktop, but it's the same issue.  We receive $X for the livestock and then expenses like trucking & levies are deducted from it.  We need a way to record the HST paid on the expenses to be recorded as ITC's paid on purchases (there is no HST on livestock sales).  I see no way to create a sales item for this as when I try, error messages pop up.  We are currently recording it as a debit to HST collected on sales and then do a Sales Tax Adjustment journal entry quarterly (when we file HST) to reallocate it.  Since this thread is older and Quickbooks has stopped replying to it, it doesn't seem that they are interested in fixing this problem.