We are running Junos with ArcPad 10 and ArcGIS for WM 10.1.1 on Windows Mobile 6.1. I have had success using the "Handheld Install" (Start>Programs>ArcGIS>ArcGIS for Windows Mobile>Handheld Install) tool to load the appropriate software onto the device. Also, be sure that you have the latest .NET framework installed as ArcGIS for WM requires it.
Be aware that you can't run ArcPad and ArcGIS for WM at the same time and use the GPS receiver unless you use something like Franson GPS Gate that takes the GPS signal and pushes it out a virtual port that both applications can connect to.