The fact that it does well in some markets and badly in other is part of the point of a trend following system. The problem is you need to trade markets where you get break even or slightly below performance because they might produce major trends. Let's look at Copper for example, this market has done bad for trend following since it started trading , only a little more than break even, but this one trend over the past 2-3 years had made this market more than work trading all this time.
Your analysis of the fact that the system has done badly over the past five years is wrong.
2000 $173,778.10
2001 $62,501.45
2002 $8,128.60
2003 $12,018.15
2004 $42,482.68
2005 $41,190.50
2006 $28,195.55 up though feb 21.
These results would make this one of the top trend following systems on this basket for the past 5 years. The 1.4 set of parameters which I originally used and released in Jan 1996 has done. It has made about the same profit over this period, but has had a higher drawdown and one losing year.
2000 $168,277.80
2001 $62,062.40
2002 $2,082.70
2003 $-4990.95
2004 $49,887.38
2005 $54,990.00
2006 $18,915.05 up though feb 21.
These results are amazing considering I am using a set of parameters originally optimized in Dec 1995!.