Comments: ** Comment from web user: ClintH **
That message occurs when all of the needed counters for that analysis are not present in the counter log. In the case of % Network Utilization, it requires \Network Interface(*)\Bytes Total/sec and \Network Interface(*)\Current Bandwidth. If one or both of these counters are not in the counter log, then it is skipped with the "Done - Missing counters in log" message. To ensure that all of the counter instances are in a counter log, try exporting a PAL threshold file into a Performance Monitor data collector template using the Export to Perfmon template file button on the Threshold File tab in the PAL Wizard. I talk about this in my blog entry at http://blogs.technet.com/b/clint_huffman/archive/2008/09/02/how-to-use-the-pal-tool-for-biztalk-performance-analysis.aspx.