1) I just did a test where all programs run on the same PC. I have VVP, plus two weather programs whose start is dependant on one of VVP's ports. After all is started up, I click disconnect on VVP. Not long after that, the StartWatch port monitor shows the port going down, then the two weather programs are shutdown. When I click Connect in VVP, the port monitor shows it's up agains, and then the two weather programs are started again. If this is not what you're seeing, then I need to find out what's different in your configuration and setup. Also, make sure you have the boxes checked in the program options that say you want to restart the program when the targget comes back up.
2) Another odd one. I have the same configuration for WeatherLink, and it minimizes everytime. Which version of WL are you running?
3) VWS is a bit of a problem child. It handles its windows (there's about 19 of 'em, you just can't see them) in a way that makes identifying the one that will act on a close message difficult. Pick the wrong window and sometimes nothing happens and sometimes it crashes VWS. I'll probably have to put some more code in specifically for VWS. Also, if StartWatch tries to close VWS before VWS is totally and completely finished initializing (which can take a while), that can also cause the close to fail. Although not an ideal solution, you can use the Close/Kill All Programs option in the Programs menu rather than the dialog that pops up when you close StartWatch. That will try to close the programs nicely, and then terminate them if they don't listen. I don't do that when StartWatch closes, because it requires waiting a little while to see if the programs close without needing the less polite termination technique.
Steve