Came across something like this before.

On the Sub Reports where you assign the Sage 100 company codes, one of the companies was in there twice.

Check to see if Company B is listed twice?

When I look at the Balance Sheet - Combined, and look at Just company A, it shows the account for Company B with the Company A Amounts, and if filtered to Company B it shows Company B amounts on both listings for that account.

Company A - filtered
Cash A - $5,000
Cash B - $5,000

Company B - filtered
Cash A - $1,000
Cash B - $1,000

Again, it is doubling any account that is listed in both companies. 

Are you talking about under "Company" and adding the two company codes? 

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I was referring to the Database Consolidation List.

In the shot above the Co Coder PRP is in there twice.

If not I would have to see the Template that the report uses.

You don't really tell us how your template is setup so it makes it somewhat difficult to address your issue. It appears that you are using the Consolidated Financial Report Designer. This requires that you add all companies to the database consolidation list in each of the subreports. It may be, as has already been noted, that you have a duplicate company code in one of these lists.

If you determine that you don't have any duplicate company codes, then it is probably how you set up your template. Did you bring over the accounts for each company into the same column and then sort? If so, you have to add the company code in the function argument. If you leave it blank it will 'assume' that you want to use both companies for each row. That would result in the cash account calculating the sum of both companies.