Hi LBaker
Thanks for your post.
You mentioned that the GST report you are using is a cash-based report, the Balance Sheet report in the desktop is an accrual-based report. As these are two different accounting methods you are likely going to find a difference in values.
There is a difference with the browser GST reports in the way it determines if it is a sale or a purchase. The desktop reports use the transaction type (e.g. Invoice, Bill) to determine if it should be reported as a sale or a purchase, this is ok unless you need to deal with recipient created tax invoice where you have lines that are coded to both to income and expense accounts.
In desktop, you would need to use custom tax codes to split this out. In the browser, the reports look at the line detail and will report the GST based on the account type, e.g. if the line is coded to an expense account it will report under the purchases area of the GST report, if income it will report under the sale.
The total GST (collected-paid) should be the same in both reports.