Answer
The layers in a map configuration file created with ArcMap (.MXD) are numbered in reverse of those in a map configuration file created with ArcIMS Author (.AXL). In ArcIMS Author the layers are counted from top to bottom; in ArcMap they are counted from bottom to top.
Example:
The .AXL and the .MXD file both include the two layers in this order (this equals the order the layers are listed in the Table of Contents):
Parcels
Roads
When setting up hyperlinks for the image service associated with the .AXL file, update the corresponding ArcIMSparams.js for your HTML Viewer file like this:
hyperlinkLayers[0] = "Parcels";
hyperlinkFields[0] = "";
hyperlinkPrefix[0] = "";
hyperlinkSuffix[0] = "";
hyperlinkLayers[1] = "Roads";
hyperlinkFields[1] = "";
hyperlinkPrefix[1] = "";
hyperlinkSuffix[1] = "";
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When setting up hyperlinks for the ArcMap image service associated with the .MXD file, update the corresponding ArcIMSparams.js for your HTML Viewer file like this:
hyperlinkLayers[0] = "Roads";
hyperlinkFields[0] = "";
hyperlinkPrefix[0] = "";
hyperlinkSuffix[0] = "";
hyperlinkLayers[1] = "Parcels";
hyperlinkFields[1] = "";
hyperlinkPrefix[1] = "";
hyperlinkSuffix[1] = "";