In Stereo Analyst for ArcGIS 2011 (and upper versions) when using imagery with four bands (R, G, B, IR) the R-G-B band combination displays correctly in both ArcGIS and IMAGINE Stereo Views, but when another combination is used such as IR-R-G the ArcGIS View displays this Color IR band combination correctly, but the Stereo Window does not seem to change.
You should be able to open the ArcMap Options dialog and select the Raster tab to set the band combinations that are used to open a multi-band image (4 or more band data source). Stereo Analyst for ArcGIS will open the image in the Stereo Window according to that setting no matter how you may have changed the band combinations in the map document after displaying the image.
Once the image is opened in Stereo Analyst for ArcGIS you can change the band combinations for the Stereo Window by going to the Stereo Layers tab. Under Stereo Window you can change the band combinations by expanding the control – you can change band combinations for both images at once – or if you expand individual images you can change the band combinations manually.
These band combinations are kept in the map document.