Thanks again for the help, I think we're getting closer 
So I added all the instances to the wsconfig.properties file and they all show up when I run the wsconfig.exe.
#JRun/ColdFusion MX Web Server Configuration File
#Mon Mar 01 13:30:00 PST 2010
1=Apache,C:/Apache2.2/conf,"",C:\\Apache2.2\\bin\\httpd.exe,"",false
1.srv=cfusion,"cfusion"
1.cfmx=true,<null>
2=Apache,C:/Apache2.2/conf,"",C:\\Apache2.2\\bin\\httpd.exe,"",false
2.srv=cf2,"cf2"
2.cfmx=true,<null>
3=Apache,C:/Apache2.2/conf,"",C:\\Apache2.2\\bin\\httpd.exe,"",false
3.srv=cf3,"cf3"
3.cfmx=true,<null>
4=Apache,C:/Apache2.2/conf,"",C:\\Apache2.2\\bin\\httpd.exe,"",false
4.srv=cf4,"cf4"
4.cfmx=true,<null>
5=Apache,C:/Apache2.2/conf,"",C:\\Apache2.2\\bin\\httpd.exe,"",false
5.srv=cf5,"cf5"
5.cfmx=true,<null>
I also did this for each instance....since they were set to true.
Open the jrun_root/servers/servername/SERVER-INF/jrun.xml file for each server instance and locate the ProxyService service. Ensure that the deactivated element is set to false
But lets say I kill the service for cf2 and/or stop it in CF Admin from the Instance Manager, the site still stays up...
Here's a sample of my Apache configs.
httpd.conf
# JRun Settings
LoadModule jrun_module "C:/JRun4/lib/wsconfig/1/mod_jrun22.so"
<IfModule mod_jrun22.c>
JRunConfig Verbose false
JRunConfig Apialloc false
JRunConfig Ignoresuffixmap false
JRunConfig Serverstore "C:/JRun4/lib/wsconfig/1/jrunserver.store"
JRunConfig Bootstrap 127.0.0.1:51020
#JRunConfig Errorurl url <optionally redirect to this URL on errors>
#JRunConfig ProxyRetryInterval 600 <number of seconds to wait before trying to reconnect to unreachable clustered server>
#JRunConfig ConnectTimeout 15 <number of seconds to wait on a socket connect to a jrun server>
#JRunConfig RecvTimeout 300 <number of seconds to wait on a socket receive to a jrun server>
#JRunConfig SendTimeout 15 <number of seconds to wait on a socket send to a jrun server>
AddHandler jrun-handler .jsp .jws .cfm .cfml .cfc .cfr .cfswf
</IfModule>
httpd-vhosts.conf
<VirtualHost x.x.x.x:80>
DocumentRoot "C:/domains/cf2"
<IfModule mod_jrun22.c>
JRunConfig Verbose true
JRunConfig Serverstore "C:/JRun4/lib/wsconfig/2/jrunserver.store"
JRunConfig Bootstrap 127.0.0.1:51000
</IfModule>
</VirtualHost>
<VirtualHost x.x.x.x:80>
DocumentRoot "C:/domains/cf3"
<IfModule mod_jrun22.c>
JRunConfig Verbose true
JRunConfig Serverstore "C:/JRun4/lib/wsconfig/3/jrunserver.store"
JRunConfig Bootstrap 127.0.0.1:51002
</IfModule>
</VirtualHost>
I also noticed that in each jrunserver.store for every instance, all that's in there is "proxyservers=" Should there be anything else?
For the most part everything looks like it should be working.
My jrunserver.store files all say the same thing as yours.
Have you done a restart on Apache and CF just to make sure things are being picked up correctly?
A couple of things you can try but I'm not sure if it will make a difference or not.
In each of your virtual hosts, remove the
<IfModule mod_jrun22.c>
JRunConfig Verbose true
JRunConfig Serverstore "C:/JRun4/lib/wsconfig/2/jrunserver.store"
JRunConfig Bootstrap 127.0.0.1:51000
</IfModule>
And just do:
JRunConfig Verbose true
JRunConfig Serverstore "C:/JRun4/lib/wsconfig/2/jrunserver.store"
JRunConfig Bootstrap 127.0.0.1:51000
Also add in "JRunConfig Apialloc false" to each of them. This will allow the stub to grab memory from the operating system rather than Apache which is supposed to be safer.
Let me know if any of those help at all.