Only thing I can think to look at is to make sure that the calls you're looking for are using jdbc connection methods that are included out of the box in the jdbc sensor pack. You can see which ones are included there by looking at the sensor packs in the server settings:
If what you're using isn't there that would be why you're not seeing them. You can also take a cpu sample when this transaction is underway to see if any of these methods show up, the sample would include everything that is executed regardless of if there is an appropriate sensor in place.
Of course always consider it a possibility that the call you're looking for is showing up somewhere that you don't expect or something unrelated to the calls themselves.