We are hydrolysing a Pentaerythritol ester of mixed fatty acids (C6 to C10), then trying to create the methyl esters of the fatty acids, using a Boron trifluoride/methanol solution to achieve esterification. This doesn't appear to work well with such short chain acids, although it is fine with longer chains.
Any practicle suggestions?

Have you tried Diazomethane ?
It should work on contact. You would have to make the Diazomethane your selfe, but that is quite simple. For further info send me an e-mail.

My lab han't had any problems esterifying C6 to C10 fatty acids with boron trifluoride/methanol, but found the "difficulty" to be to force the esters into non-polar solvent like petroleum ether for GC assay. We esterify, add some PE, then add saturated NaCl solution, then mix to force the smaller esters out of the water-methanol portion. Some ethyl ether can be mixed into the petroleum ether too. Propyl and butyl esters work also.

Related to this thread is a question I've had for awhile: what are the reasons that the most common way to do fatty acids by GC is to make the methyl ester and not the silyl ester, which is very simply done with BSTFA or something similar?

Trimethylsilyl diazomethane (a diazomethane substitute)works nicely too, and you can buy it off the shelf from Sigma-Aldrich.

For my particular application I found methyl esters too volatile, so I used MTBSTFA. If you are using GC-MS this gives you a fragment characteristic for the mw of your acid so is useful for helping to identify your particular acid if you need to.

Spencer, I've worked in the soap and food businesses, and the traditional American Oil Chemists Society (AOCS) test method Ce 1-62 uses methyl ester formation, then GC assay. An advantage to this (on the correct polar columns is that the saturated fatty acid methyl esters elute before their corresponding unsaturates (for example, C18 stearic, then C18-1 oleic, then C18-2 linoleic). We've also used trimethylsilyl derivatives on a nonpolar column, where the elution order is unsaturates first.