I sew over the pins all the time and even when I hit one with my needle it doesn't usually mess anything up. I just go slow over them that's all.

This isn't a stupid question. Lots of people will blame timing for things that aren't. It's a good thing to know!
Yes, pins can throw timing on a machine, so can overly dense stitches (think an embroidery pattern sized too small, and the thread builds up, or satin stitching, same problem) It's way more common to throw timing on a "newer" machine if only because they have rubber or plastic gears that can flex, or crack. The older machines were metal gears, so they are harder to flex out of the way, or force apart.

a machine with a timing can skip stitches - but so can a needle in the wrong way. Sometimes it'll do it only on some fabrics and not others, which can be hard to figure out.
it can not pick up the bobbin thread or only does it sometimes
it can, if the timing is far enough out, smash needles on parts of the hook

I'd say if your machine is working OK, it's probably not out of time.

If you want to know more about timing, and how to check it, in layman's terms, I wrote a series of articles on it in January, they start here: http://www.archaicarcane.com/2013/01...have-the-time/

Ugh. I meant a machine with a timing problem can skip stitches

Haha, not sure if I have interpreted correctly but it sounds like you are describing how I always put pins in because I am left handed! Lol. Mine are put in the opposite of right handers. Guess that's one advantage of being left handed.

When I bought my Viking (1998) the dealer told me never to sew over pins as it could cause a problem with the computerized board in the machine. So I either pin back from the seam line or remove them as I come to them.

Try one of the decorative stitches and you will probably see what happens when the timing is off.

You don't need a new sewing machine to do this, I rarely pin and when I do I remove them before the needle, I butt up, make sure the stretchy (off bias part) is on the bottom and let the feet dogs eaise it in. Most of my quilt piecing and quilting is done with my 1934 White Rotary and Singer Featherweight, both of them do a far better straight seam and more dependable then my new sewing machine.

Yes, that's how I found a small timing issue a couple of weeks ago. The machine would straight stitch like a dream, but even a zig zag stitch would skip all of the right side stitches.