Associating payments with a loan

I've got a loan (on my vehicle) that I had previously set up so that payments I was already making start automatically getting applied to the loan by Quicken. Quicken determines how much of that payment was
applied to the principle and to the interest and every time my automatic payment went out, Quicken knew to apply it to my loan. That stopped in July. I had 2 more payments go out that somehow Quicken did NOT apply to the loan. I can't find anything, anywhere in the software to set this up. My loan is now paid off, but the last 2 payments didn't get applied to the loan, internally per Quicken's book keeping.
Also, I'm entering another loan that just began a few months ago and still has a while to go. I can't find anywhere in the software a way to connect those payments to the loan.
I should mention that I use PC Banking (built into Quicken) to make all of these payments, so I set up the payment once and set it to automatically pay on a regular schedule. I would like the payments to be connected to the loans they're paying off so the loan balances decrease appropriately as payments are made. This /was/ working on the auto loan, /is/ working on another auto loan and 2 mortgages, but I can't get it stopped working on one auto loan and I can't get it started on a fairly new loan.
Anyone know how to do this?
TIA
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