@Mubali if you rename your patches to MUB000.BIN (previously MUBSI.BIN) and MUB001.BIN (previouly MUBSA.BIN)
it does work!
Carefully follow this post https://sebiik.github.io/community.axoloti.com.backup/t/tutorial-how-to-change-program-on-axoloti-from-external-controller/969
I had already had these saved on the card under the proper formatting, but still encountered the same issue. I just resaved the axo patches to reflect the same name MUB001.BIN and MUB002.BIN and received the same issue. Patch will play for a second, then when trying to switch patch, can't play anything else
they work for me too...
I didn't bother renaming the patches, I just used card reader mode to rename them.
which version of axoloti are you using?
@keyman , were you using the released 1.0.6 version?
if you start the patches in live mode, does it switch away... or keep running the patch?
Im a bit lost, patches seem fine, the only think I can think of is:
Im assume your using the latest version of the Axoloti software, and that is one of the release builds (1.0.6)
(I'll confess I'm using a development version, but this is unlikely to change the functionality)
the entering sd card mode is a 'red herring', I think this is just because you are restarting the axoloti board, you would get the same if you power cycle it.
can you let us know more about your setup, e.g. which OS, which version of Axoloti etc... not that it makes a difference, but still good to know.
Well, oddly enough after a couple of reboots and placing my patches back on the card, it seems to work again. Not sure exactly why it freaked out. I'll check to see if my start.bin has the patch switcher in it. I'll make sure it does just in case, but now it seems to work and I don't have the controller object enabled at all. So at least having the patch change in the patch itself seems to work for the time being. It started working again once I provided separate power for the axoloti instead of powering it via a powered usb hub. Well, it's working now, so we'll see if anything else happens.
??To rename or not rename... I was also referring using card reader mode 
yep!! 1.0.6 (bring on a new version) 
Not sure if its for me; going live with say MUB001.BIN (MUBSaw osc basic.axp) and then send program ch 2 switches for
MUB002.BIN (MUBSine osc basic.axp) and the back and forth; if you do send prg 3 or say 99 it "disconnects" (maybe adding some empty/dummy patches do the trick, if needed)
It is a bit messy 
but only a matter of getting used to, future "how to" will help.
Sending patches to SD card and having to rename them... I'm sure this will improve in some new versions.
Oh @thetechnobear and adding @jaffasplaffa Program Change to a controller object patch works great!!, throw in some empty patches (with controller object ) and now I can have 16 PRG Categories!!)
example
00 to 07 LEAD
00-saw
01-sine
02-triangle
03-supersaw
04-empty
05-empty
06-empty
07-empty
08 to 15 BASS
08-simplebass
09-empty
.. you got it by now... and replacing empty for new patch, as you go along
hint: johannes is adding some extra functionality in this area for the new release, which will make this much easer to manage 
Did the extra functionality in this area for the new release ever materialise do you know ?
Is this a reference to PatcherBanks ?
I'll admit that I am currently stumped. Can't understand this controller object thing at all. sorry., I can see your explanation is detailed,. I just can't get my head around it at all