Short answer
Both of these symptoms usually come from the same cause: a binder that hasn't yet had the adjusting entry that agrees its books to the tax return. On a tax (e.g. 1120S Schedule L) balance sheet, current-year net income does not roll into retained earnings on its own — you post an adjusting journal entry to close it. Until you do, the balance sheet is out of balance by exactly the current-year net income, and any prior-year comparison that reads from that binder shows the same un-adjusted numbers.
"My balance sheet doesn't balance (Assets ≠ Liabilities + Equity)"
First, a quick self-check that tells you almost immediately what's happening:
Is the amount it's off by equal to your net income (revenue − expenses) for the year? If yes, this is expected until you close it.
Right after an import, the trial balance itself balances (debits = credits), but the balance sheet won't, because current-year earnings haven't been carried into equity yet. Tax balance sheets map equity to lines like Retained earnings – unappropriated; they don't include a "current year net income" line automatically.
Fix: add a "To agree to tax return balance sheet" adjusting journal entry in the binder (this is the entry that closes current-year income into retained earnings and reclassifies anything else needed to agree to the return). Once it's posted, the balance sheet ties out.
If it's still off after that, the next most common cause is an account sitting in the wrong section (for example, an asset coded into liabilities). Check that each account is mapped to the correct balance-sheet section.
"The prior-year comparison doesn't match the prior-year binder"
The comparison column on a report pulls its prior-year figures directly from the prior-year binder you selected (Settings → Show Comparison Columns). So the comparison is faithfully showing whatever is in that binder.
If the prior-year binder hasn't been balanced/finalized — i.e. it's still missing its own "To agree to tax return balance sheet" entry — then the comparison column shows those same un-adjusted numbers, which is why it can look like it "doesn't match" what you expect. It matches the binder; the binder just isn't finalized yet.
Fix: balance the prior-year binder first (same adjusting entry as above). Once the prior-year binder is in balance, the comparison column lines up automatically.
How to confirm which one you're hitting
Open the prior-year binder on its own and look at its balance sheet. Does it balance?
If it doesn't, note the out-of-balance amount and compare it to that year's net income — they'll usually match.
Check that binder's journal entries for a "To agree to tax return balance sheet" entry. If it isn't there, that's the missing piece.
Still stuck?
Send us the trial balance date/year for both binders (and the exact amount the balance sheet is off by) and we'll pinpoint it quickly — or we can hop on a short call and post the adjusting entry with you.