So many settings, so little time...
When you mentioned targeted settings, I was looking on the new server, and didn't see anything. When I did the original migration test, the new server was set to use HTTPS, and I changed the targeted setting on the old server to use HTTPS.
In testing another migration this morning, I double-checked the old server settings and found the HTTPS there. I changed it to HTTP, added the client to the migration collection on the old server, and it showed up on the new server almost immediately. Once on the new server, it installed pcAnywhere before installing the SMA. I'll have to make sure other plugins/agents are disabled during the actual migration.
A little off topic, but one thing I did notice is that the computer received a different GUID when it reported in to the new server. I'll have to remember to test another migration after I import our Asset Management information. I'd hate to have to re-enter all of that information.