They are usually both right, and they are answering slightly different questions.
Where the difference comes from
Different sources. Your accounting software knows what was recorded in it. Omnyra reads that and your bank, your card processing and your field service system. Anything present in one and not the other produces a difference.
Different timing. An invoice raised today is revenue in your books immediately and cash at the bank in forty days. Which one a figure counts depends on whether it is a cash or accrual view — see cash and accrual.
Different treatment of duplicates. The same payment can legitimately appear in three systems. Omnyra counts it once and treats the bank as authoritative on cash. See the unified ledger.
Why the difference is shown rather than reconciled silently
Presenting your accounting software's figure as the answer would mean repeating its mistakes back to you with more confidence than they deserve. Where the two disagree, the gap is named with the amount attached, which is less tidy and more useful.
Sources is where to see it.
Which one to use for what
Filing and formal accounts — your accounting software, produced with your accountant. That is what it is for.
Operating decisions — Omnyra, because it sees the bank and the jobs as well as the books.
Cash today — the bank, always. See real cash balance.
When a difference is worth chasing
A small one that resolves within days is timing. A persistent or growing one means something is recorded in one place and not the other, and that is worth finding — see books versus bank variance and reconciliation.
Before you conclude anything is wrong
Check the period and the basis. Most reported mismatches turn out to be month-to-date against last month, or cash against accrual. See a number looks wrong.