arbor I think I have a good idea about what is going wrong.
You are using kill -9 on a wine process are you not wine c:\\windows\\system32\\taskmgr.exe or wine c:\\windows\\system32\\taskkill.exe [wine internal pid]
Issue with be a confused internal emulated pid table in wine.
wineserver -k or use wine own internal methods to kill. Using Linux or OS X or other host options don't end well.
wineboot is a highly miss understood command.
http://wiki.winehq.org/wineboot
wineboot with no options does not kill any processes. If anything it starts processes. Yes some badly coded applications services running wineboot after wineboot will slow you system down because you end up with the 1 service running many times. This is why I recommend 1 application if possible per prefix.
"wineboot -e" followed by "wineboot -f" should be attempted. As this asks applications to quit cleanly is the -e option -f option then goes after those that don't. Yes they have to be run in order. -f flag only works on those applications that have been told to quit that have not quit yet. Yes you said you have attempted all options did you do these options in the exact order.
"wineboot -k" is close to "wineserver -k" in most case I find wineserver -k more dependable.