I'm bringing up this old thread to add my own bagel issues to it (so others looking for bagel help can have it all in one place!).

I made bagels yesterday, using Suzanne's recipe.  I had no trouble with my yeast, with the dough, nor the initial rising.  Here is how they looked before boiling:

So far so good, or so I thought…

I boiled them up, had a little bit of trouble getting them up off the parchment to put in the boiling water.  I'm so used to not disturbing rising dough I was so afraid they would deflate, which they did, but not until I baked them–they rose beautifully & expanded in the water. Enough so I could not do 3 at a time, had to do 1 at a time.  I didn't get pictures of the boiling stage cuz I don't have a third hand ; ))

It was in the oven they slowly fell, and fell even more upon cooling out of the oven.  Here's what they looked like after baking:

They had funny clearish spots that weren't wet, just almost see-through, and then a few wet doughy spots, in the center or on the edges, which didn't bother me.  I just cut those out and ate them anyway, but I want them not so flat!

3 things I think may be the culprit:

1. They may have over-raised so that by the time they hit the oven they collapsed. Which I find weird that they puffed in the water, but then fell in the oven.

2. The dough may have been too wet though it was just barely tacky. From what I've read other sites the dough shouldn't be tacky at all.

3. With my hard water I sometimes have trouble with recipes and wonder if boiling 3 mins per side as called for in the recipe was too long in this hard water. I researched and found other recipes for bagels called for only boiling 30 sec each side (just read Nerosmom's recipe and hers calls for boiling for 45 sec).  I did notice that the bagel looked really stretched and the dough begin to fall apart the longer I boiled it.  

Even like this they were absolutely delicious, and I look forward to better bagel success in the future.  Next time I'll boil for a shorter time and try the lid trick northcountrygirl recommended. 

Update: I just found this link with great information on specific techniques for making bagels.  He does say that bagels that don't sink when first put in the water are over-raised, so i think that was my issue. 

"The bagels should sink to the bottom of the water. If they float at once, they were allowed to rise too long. After a few seconds, typically less than five, they should float to the top. If they don't, nudge them with a spatula, sometimes they will stick to the bottom of the pan. After a minute, whether they floated or not, flip them over. Give them another minute.

For your next batch: if the bagels never floated, or took more than a minute to float, let them rise a bit longer, give them a bit more floor time or use a warmer refrigerator next time. If they floated too quickly, let them rise a bit less, give them a bit less floor time or use a cooler refrigerator next time. If you are making a larger batch and your bagels never floated, let them rise a bit more at room temperature before you boil the rest of the batch."