In general, anything heavy on raw puff will keep it from puffing. There are some butter pastries where they brush on this or that kind of flavor goop (including chocolate, but most of the ones I know are filled at the end. I've never been to Panera, so googled it. The pictures I saw looked piped. There are also many entries for "recipe" where other people have tried to replicate them. You might want to read them through and at least eliminate that which has been done. There are also a number of pain au chocolate recipes that do use solid chocolate.

I've never had Panera's but some searching makes me think you might want to follow this recipe -- they use an egg wash before adding the chocolate, so maybe that 'seal' makes a difference when baking?

That is practically what I did. Panera's chocolate pastry is made with croissant dough giving it a good chew. Using puff pastry, I used the egg wash over the final assembly. Next time will be before rolling. I did use milk, as I do with apple pie crust, to seal it though.

I also experimented with a small rectangle of baked puff pastry dough under the chocolate before the final wrappingand it worked very well.

A second trick was to cook the pastries on a cooling rack and not directly on the parchment/cookie-sheet.

There is no telling which new idea did the trick.

I did not get any pics as they evaporated before I could power up my phone....

It is very interesting the puff pastry dough package did not explain what size the dough would be. After cutting the pieces to what I wanted, I rolled them out to double the length for better rolling and sealing.

The rack was good because the moisture from the dough can accumulate on the paper and make the dough gummy. Air circulation is better. :)

Congrats on the success! Is it the flavor you wanted?