Should an EIDL loan that is a checking account be listed on my balance sheet as an asset and then again as a liability, is that correct?

The EIDL loan should only exist as a long term (30 year) liability. This loan has no forgiveness component, only a possible non-taxable, non-repayable "grant" in the form of an advance.  How you treated the deposit of the funds into your banking is probably the issue.

Lets presume that since you do have a liability for the loan that you did in fact receive the funds and they were deposited. You have to look at that transaction to determine what needs changed. In simplest terms you would have a Deposit into whatever bank account received the money and the line item (source) is the loan. Receiving a loan increases two accounts, current asset banking, and and a liability account for the loan.  Debit banking, Credit liability.

Did you (in error) enter the loan details with an opening balance? No loan should ever be added to your books with an opening balance unless it actually has an opening balance (such as when converting from one software to another or adding an existing loan forgotten about)  Without seeing your actual transactions this is my best guess as to the problem. By entering the liability with a beginning balance there had to be an asset offset in equal amount, thus the creation of an asset for the EIDL