This part is interesting:
2013-06-05 15:31:51,979 DEBUG zen.zenprocess: Found new httpd.exe httpd.exe af5f979fd45fdd80441276b75378f2db pid 1384 on app-01
2013-06-05 15:31:51,979 DEBUG zen.zenprocess: Found new httpd.exe httpd.exe af5f979fd45fdd80441276b75378f2db pid 1212 on app-01
That means the running processes have different pids than when first modeled. Which is normally fine.
Try to delete the httpd processes and remodel.