im sorry your having these issues. The only problem i can see is your trying to run multiple displays on a single display. Although I allow it to work in the code, it is really not designed for this or tested like this.
PinballX does try to hide the desktop, so it may not be slow starting vpx, just that pinballx is hiding it. is it certain tables?
if things are slowing down it could be a memory leak, but hard to know if that is PinballX or it is caused by an external component or plugin such as flexdmd.