I'm facing a similar sort of problem/question, but involving a PXI running LabVIEW RT. I believe that when you use VI Server, you are basically running, not an .EXE, but rather a LabVIEW .vi file. As I understand it, the way to get an .EXE running is to (at least on the PXI) make it part of the "Startup" procedure for the remote device (I believe this means calling it "Startup.Exe", and putting it in the "right place"). The main point is that this is not something that you "start", but rather something that you "build in" to the system.
Note that once you have an "executive" running on the RT system, whether you "build it in" to start up with the machine or get it running some other way, it should be possible to have it dynamically load in other routines that you FTP down. Will this work for you?
An alternative is to have the "executive" be an ordinary vi that you first download to your target. You can then start it running with VI Server (this is, in essense, what we're doing with the PXI).