EDIT PART WITH FIX
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I spent so many hours trying different drivers midi mappers and different MPU-401 options and i simply can't believe what is actual solution to this problem
A guy came to RetroArch discord, asking is there a way to change controls in RertroArch for windows 3.1 games in dosbox, but while i was writing answer for him he figured it out on his own
Then i asked him could he try to run Zombie Wars and check does music plays properly.
And to my surprise it did and he had fresh installation of windows 3.1 he didn't even know how to change resolution
So i told him how to do so, and what turned out?
After changing resolution music get same bug i described below
And believe or not actual music problems comes from 2 things
1st - MPU-401 port is occupied/used by something in dosbox (i don't know exactly what it means other than like trying to delete mp3 file from your desktop while it's playing, and you can't because you will get message something else is using it)
2nd - Resolution is too high or simply it's not set to 640x480
And that 2 things need to be adjusted for music in Zombie Wars In windows 3.1 in dosbox actually work properly

So what is the solution here?
First the MPU-401 port
IF you use frontend like me (DOSBox Game Launcher) you simply edit profile of a game (windows 3.1 in this case) go to sound tab and next to MPU-401 port select NONE
IF you are using DOSBox alone then go to game config file and simply change this line
mpu401=
to this
mpu401=none
And save

Now for resolution
Simply in Main>Windows Setup>In upper left corner Options>Change System Settings>Display> S3 Trio resolution of 640x480>hit ok and restart windows
I did try 256 and 32k and both works fine

And now you will have properly working music in Zombie Wars
I still can't believe resolution was affecting it but whatever im happy it works and i hope it will help someone

Screens in case someone need them

Just a quick note here
I still have music issues launching it under dosbox in windows 7
Even when im using RetroArch with any of 3 available dosbox cores (ON WINDOWS 7)
If i leave game untouched after launching it and get to screen that says Halloween Harry in Zombie Wars
Music kinda like starts keep playing but on top of that same instance of the track is starting to play from the beginning while i do hear like 1 note hang in there that keep playing
Same crap happens in missions
But like i said i needed it to work only for android im using Magic Dosbox and RetroArch and on both emulators it works just fine (of course with MPU-401 disabled) (ON ANDROID)
But for whatever reason on RetroArch on android i can launch windows 3.1 i can launch zombie wars but then i get error like "can't create bla bal bal \zwars.bin" or something like that
Solution was to simply move whole windows folder to my phone memory storage instead of trying to run it from SD Card
I simply placed it in download folder on my phone and then went to RetroArch added it to playlist and works just fine (now i got it in phone>pc>windows and it still works just fine)
While in Magic Dosbox it works just fine no matter where i place windows folder even on SD card
If someone really need it to be playable on windows (HOST) i suggest using PCem i have different graphic card i can go to any resolution and i don't need to disable MPU-401 port and Zombie Wars works just fine
(that's why Virtual MIDI Synth works just fine)

Fun fact
I have Nox Player (android emulator) on windows host
And when i installed in that nox magic dosbox set up all configuration just like on my phone even copied windows folder from my phone back to my PC and then mounted it in magic dosbox in Nox player
I still have exact same music issue
I start to believe problem is more with my windows 7 or windows overall more than it is with dosbox itself well idk what's the truth here
But on PCem it works just fine on Windows 7 screen to my PCem and Windows 3.1 that runs Zombie Wars perfectly fine below

(I spent yesterday like half of a day trying to get that windows 3.1 to run on some guy's magic dosbox and retroarch from retroarch discord just because of his 1 mistake
If you have folder like windows 3.1 and in it is whole windows folder and rest of the file like where it looks like Windows 3.1\windows
Then you don't mount Windows 3.1\Windows you actually mount Windows 3.1 folder as your drive C
That windows 3.1 folder could be named anything but just because it's also named WINDOWS he assumed he need to mount one inside it not realizing he is mounting actual windows directory as drive C
It simply could be named like OldGames and it would be OldGames\Windows then again you mount OldGames as drive C not OldGames\Windows
So take it as quick tip)

Screen explaining what i mean

PCem and Windows 3.1 running in PCem configuration
If you want to insert some files into it option A is using ZIP image (Im basically doing what this guy describe https://www.youtube.com/watch?v=xAk_-AeTJec
Option B for me is simply mount that windows 3.1 disk image as slave on my windows 98 in PCem and then i simply insert files from one drive to another and use Iomega ZIP disk if i wan't to extract something
Since i have problems mounting Iomega zip disk to windows 3.1 directly)

ORIGINAL POST BELOW
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So in short of it whenever i launch Zombie Wars from win 3.1 in DOSBox music in menu skips to the end after like 2-3 secs and then just stops playing
While in missions it like plays for 2 or 3 seconds and then just stop and plays note on which it stopped
It's midi music and on other hand sound plays just fine
While midi files in media players in windows 3.1 plays just fine

Anyone have any idea what could be possibly causing that?

I can provide my config but i have pretty much exact same config i use for any other game

Here is my sound config but like i said i kinda use it for every single other game i run

I feel like there is some configuration to do on win 3.1 to do but my knowledge just isn't enough for that

I just want to add that exact same game works just fine on PCem on win98 i mean that music

--Edit--
I copied whole windows 3.1 folder to my phone and run it with Magic Dosbox
And on my phone music in zombie wars plays just fine but the sound is repeating like each half second not playing other sounds

So it looks like i have problem with dosbox itself and not windows 3.1
But funny how i use exact same configuration on PC and Android for command & conquer stargunner war diary tyrian 2000 and z (zed) as for win3.1
Yet somehow i have different result?

--Edit 2--
I was able to set up win 3.1 on a drive with ms-dos on PCem and turns out music in Zombie Wars works just fine
So yeah it is problem with dosbox configuration and all i find over internet about it is whenever ppl mention that problem with midi music on windows 3.1 dosbox
I always see something about MPU-401 conflict and port 330 and suggestion to disable it
I did set it to none so what else i can do?