I don't know if I've well understood your issue.

The first think coming in mind is that decimal accuracy for Product Price is set to 2 on Odoo. Obviously if you change the decimal accuracy on

Settings --> Database Structure --> Decimal Accuracy

you'll change it globally. If you just change to 4 digits to subtotal field I think Odoo will add just two '0' to the right because the rest of the fields were saved with 2 digits. Try to set 4 digit globally, create an order and see how Odoo compute it.

Second thing I can think is that somewhere Odoo do a round for values on module. I don't know in wich one you are working, you need to have a look on it yourself.  

Edit:

The solution of your problem could be on sale.py. For example:

    def _amount_all(self, cr, uid, ids, field_name, arg, context=None):
        cur_obj = self.pool.get('res.currency')
        res = {}
        for order in self.browse(cr, uid, ids, context=context):
            res[order.id] = {
                'amount_untaxed': 0.0,
                'amount_tax': 0.0,
                'amount_total': 0.0,
            }
            val = val1 = 0.0
            cur = order.pricelist_id.currency_id
            for line in order.order_line:
                val1 += line.price_subtotal
                val += self._amount_line_tax(cr, uid, line, context=context)
            res[order.id]['amount_tax'] = cur_obj.round(cr, uid, cur, val)
            res[order.id]['amount_untaxed'] = cur_obj.round(cr, uid, cur, val1)
            res[order.id]['amount_total'] = res[order.id]['amount_untaxed'] + res[order.id]['amount_tax']
        return res

 And

 def _amount_line(self, cr, uid, ids, field_name, arg, context=None):
        tax_obj = self.pool.get('account.tax')
        cur_obj = self.pool.get('res.currency')
        res = {}
        if context is None:
            context = {}
        for line in self.browse(cr, uid, ids, context=context):
            price = line.price_unit * (1 - (line.discount or 0.0) / 100.0)
            taxes = tax_obj.compute_all(cr, uid, line.tax_id, price, line.product_uom_qty, line.product_id, line.order_id.partner_id)
            cur = line.order_id.pricelist_id.currency_id
            res[line.id] = cur_obj.round(cr, uid, cur, taxes['total'])
        return res

Where round function is used on all related voices you need to change. Since those are computed values the global decimal setting do not works. Good hunting.