M-1 and M-2 amounts are different

I assume you mean by the M-2 balance being off that the ending balance on line 9 is not equal to the balance sheet amount in line 21 of Schedule L, Partners' capital accounts. 

The M-2 schedule should show the beginning balance equal to the ending balance from the previous year. To that you add income stated on the tax return, deduct distributions to the owners, add capital contributed to arrive at the ending balance. You may also have other adjustments for income or expenses that are on the books but not on the tax return, or vice versa. So, you need to look at those entries and determine which one of them is wrong to resolve your issue.

The loan from the partnership to the partners should not affect their capital accounts so it shouldn't appear on the Schedule M-2. The book entry for that would be a debit to loan receivable partners and credit to cash. You need to make sure it isn't included on line 6 of schedule M-2, distributions.