The whole point of freezing is to know what counts and valuations were in Sage before the count. The whole point of the count is to get the real world to match the computer world. But it still requires that you know what is to be counted. That's a task in and of itself.
When things physically come in and go out after the freeze, those items have to be excluded or included during the count itself or you still lose track of what that count should be. Usually, it's this part that messes up the variance report. It's one of the reasons you'll see the variance register adjust an item up in one month and then down again the following month for the same quantity.
I've seen this messed up so many times over the years it's just a matter of course that I tell people, shut your company down, throw everyone in the company at the count process and get it done so you can switch everything back on and go back to business. The ones who follow that advice actually get very good counts with few adjustments.
Fortunately, these have always been small companies who can do their count in a day or two if they retask every employee to the count process. One large company I worked for took that advice, shut down from a Friday to a Monday night, paid everyone a lot of overtime, pizza and beer in order to count for four days straight to accomplish a 60 million dollar audited physical inventory over 9 warehouses full of tens of thousands of SKU's, etc.
The heady days of accounting, eh?