I have been making my own barbecue sauce.  As of yet I have not been able to make the sauce thick enough.  When I do achieve the right thickness and process bottles in a pressure cooker, the thickener I use breaks down and my sauce is the consistency of water.  Any suggestions on the best thickeners to use?

--Bob

Since you didn't say what you are using as a thickener, I can only speculate that it is a starch of some sort.

Starches are made up of two kinds of molecules; amylose which is a long chain of glucose molecules, and amylopectin which is also made of glucose molecules but with a ramified or branching structure.  In plants, starches are deposited into granules which contain many starch molecules.  While amylose is water soluble, amylopectin is not.

When a solution containing starch is heated, two things happen.  First, the amylose molecules dissolve into the water where, because of their length, they form a tangled mesh which traps the water and any other materials.  At the same time, water infiltrates the starch granules, causing them to swell.  All of this typically happens in the range of somewhere between 120°F (49°C) and  180°F (82°C).

Your problem is that, as the starch-thickened mixture is subjected to prolonged cooking at higher temperatures, the starch granules rupture releasing their trapped water back into the sauce.  Also, some of the starch molecules begin to break down into smaller fragments which are less able to form the mesh which thickens the sauce.  The breakdown of starch molecules is encouraged by the acidity of the sauce.

Unfortunately, there is no good way around this problem, especially for the home cook, other than carefully cooking your barbecue sauce down until it is thick enough without the addition of a thickener.  It should be boiled gently until the volume is reduced by half or until the mixture rounds up on spoon without separating.

A recipe for barbecue sauce suitable for canning developed by the USDA can be found at http://www.uga.edu/nchfp/how/can_03/bbqsauce.html.