It is because the fruit is lighter than the syrup part, so it floats. No way to keep it from happening all the time. You are doing right by letting it sit and then stir again before filling the jars. You can also try to gently swirl the jars as they are cooling. Sometimes that works.
Strawberry is notorious for this.

If it's a traditional preserve, you can bring it almost to the jell point and then let it rest overnight. Reheat the next day and finish the process. This allows the fruit to absorb more of the syrup; it helps weights equalize.

The other option with commercial pectin is to prep the jam but don't add pectin. Again, let rest overnight then reheat, add the pectin and finish.

Either way, I personally am comfortable not refrigerating but allowing to cool naturally due to the high acidity and high sugar content. Don't put on a lid. You'll have condensation and just have to cook more to evaporate it out. You can cover with a cloth to prevent any foreign matter from entering. Or if you have it, use a spatter screen.

Carol

I often use Carol's method of allowing the jam to sit overnight and then heating and processing the next day.

However, I did just make a batch of strawberry and had floating fruit. As LindaLou mentioned, I periodically swirled and turned the jars (carefully, so as not to disturb the seal), and as it cooled and thickened, the fruit settled down into the bottom of the jar.

I do that with Habanero Gold too, swirl while cooling to evenly distribute the beautiful little floating bits of pepper, apricot and onion.

Annie

This may be a no no but I did this yesterday whem I made 7 batches of Strawberry jam. One batch seemed a bit runny when I took the jars out of the HWB. After I heard them ping, I turned the eight jars upside down and left them for 20 minutes and then uprighted them. All the jars stayed sealed and the fruit is not floating. I fugure, if you can swirl it, you can turn it upside down.

There are some studies that inversion weakens the seal and increases the likelihood of a lid popping at some future point.

But frankly, with jam it's not a big issue. It's not going to affect food safety. Good preserves usually get eaten too quickly to be concerned about optimal shelf life anyway.

Carol

While they are cooling after being capped and run through the BWB bath I flip the jars over a few tines. Soon the jelly/jam sets and will hold the bits in suspention. Kind of like getting jelly to set soft, then stir in fruits, and it will solidify and hold them in suspension. Not a good idea to allow the jelly mixture too cool some before putting into jars, as it reduces the safety and vacuum seal a little.

Wow, some great ideas and advice from the experts!

I do have a question for Carol. When not adding the pectin until the next day, if using powdered, do you add it before heating it up or do you use the liquid kind after bringing back to a boil?

Elaine

I would use whichever option is most appropriate for the type of pectin you have.

It is easier to set-and-rest traditional preserves, where no commercial pectin is used, and then second-easiest with liquid pectin. With powdered pectin that's added earlier you may want to "half-cook" the sugared fruit mixture, cool and rest, then stir the powdered pectin in and continue cooking. The main thing is to get the sugar dissolved and a syrup formed so that the fruit can absorb and the weights can equalize.

You may have to play around with this a little. While I use commercial pectin occasionally, the overwhelming majority of the preserving I do is traditional and doesn't call for it.

Carol

In answer to vall3fam,
my rule is NEVER to mix different kinds of pectin in the same batch.
Regards Jim in So. Calif.

I don't think she was talking about mixing pectins, was she? Just using one kind as opposed to the other?

Carol

OK, I have read all the comments above and I have gone in and turned my jars upside down. I will leave them that way for about 15-20 min and turn them back and see what happens. This is my first time with jam, is it possible to empty all jars in pan, add more peaches, cook a bit and re-can them? If so, what do I do about more pectin. My recipe called for the liquid and I doubled my recipe. It just seemed like there was too much liquid when I filled the jars and not enough peaches. Please help!!

I was wondering the same thing. I made mine based on the certo liquid pectin insert. I followed the instructions and my jam separated, with peaches at Top. It has cooled and I know this is ok, but I really want it to be pretty for Christmas gifts. Is there anything I can do short of reprocessing? Can I warm the jars in water (or the dishwasher) and then flip them as they re-cool? I really don’t want to add more sugar as it’s sweet enough. Should I add more fruit and reprocess or just accept that they are fine as is? Thanks