[begin epic saga odyssey verbose mode post]
Boy howdy, you've all got great suggestions & I've exhausted them all (and then some!) & not tuned this in.
The basic problem is this: MaLa loads quickly, while CPWizard loads slowly, so if I launch them simulataneously or near-simultaneously, then MaLa inevitably loads faster & when CPWizard finishes loading, it steals focus.
No combination of shell combo loads, MaLaLauncher, FocusLogger, etc worked for me. (scroll to bottom of post for failure list).
So, I really just need to launch CPWizard, delay for x seconds, then launch MaLa. That's the secret.
So, I changed the shell back to explorer, clicked "run on startup" in CPWizard to make sure it would launch ASAP, & made a bat file like this & put it in the Startup folder:
start /wait c:\windows\sleep.exe 40 /MIN
start c:\emulators\mala\mala.exe
sleep.exe is a little download I found after failing to get a ping-based delay to work right. "40" is how many seconds I wait (need to trim that way down--have yet to optimize it).
This works fine. Phew!
But!!! There's one catch--after the Windows desktop loads, it pops up a command line window for the batch file & then another command line window while sleep.exe runs. Pretty ugly.
After lots of searching around, I found a nifty app called cmdow:
http://www.commandline.co.uk/cmdow/It lets you tile windows, minimize windows, launch bats in a certain window state, etc. etc.
Alas, although I can pass arguments to the program being launched with cmdow, I can't seem to send it the command of start /wait & then a program name & its argument, so I can't have it run the sleep program, wait till the sleep program's over, and *then* launch MaLa.
So, I need TWO batch files & I still get 1 command line flicker for a brief instant when Windows loads.
The 2 magic batch files:
runmalasleep.bat is in my startup folder:
cmdow /run /hid c:\emulators\mala\malasleep.bat /ma
[the /ma is just for good meaure to minimize all windows at this point, even though there's no other window open...]
and malasleep.bat is as follows:
sleep.exe 4 [4 seconds turned out to be the magic number]
start c:\emulators\mala\mala.exe
[yes, I know, I don't have start /wait on the sleep.exe 4 command, but it works great--if I add start /wait before sleep.exe, then I get an extra window popping up.......and if I just try to run sleep.exe 4 via cmdow & then have the next line launch mala, it launches both simultaneously]
Oh wait, did I forget to mention

?
Thanks,
-Jason
Appendix 1:
Here's what I tried & the failure results:
shell: mala + focuslogger & malalalauncher of cpw -> no focus
shell: cpwizard,mala + malalauncher of cpw -> works but CPW not minimized
shell: cpwizard -minimized,mala + malalauncher of cpw -> no focus
shell: cpwizard -minimized,mala + focuslogger & malalauncher of cpw -> no focus
shell: cpwizard -minimized,mala + focuslogger -> no focus
shell: explorer + mala & cpwizard in startup folder -> works but CPW not minimized
shell: explorer + mala & cpwizard bat in startup folder -> no focus
shell: explorer + mala & cpwizard bat in startup folder & focuslogger-> no focus
shell: explorer + mala/cpwizard combo bat in startup folder & focuslogger -> no focus
shell: explorer + mala/cpwizard combo bat in startup folder -> no focus
shell: explorer + mala in startup folder + cpwizard "run on startup" checked -> no focus
shell: explorer + mala "start with windows" checked + cpwizard "run on startup" checked -> no focus
try making bat file to launch cpwizard then mala, with a delay in between:
1 ping command didn't work
2 download sleep.exe -- success!!!