If you just started working out, you might just need to get used to the exercises some... although joint pain right off the bat does not sound right. As other have suggested, do not let your knees go past your toes if you do regular lunges.
As an alternative (and a fave of mine) instead of stepping forward into a lunge, actually step back. I find it is a ton more comfortable on your knees that way with a lot less stress.
It's hard to say overall what the problem is without actually seeing your form.
On a separate note, it sound pretty odd to have a kind of weakness in your knee joint itself (unless you have some kind of problems that are undiagnosed).