How does it fail? Does it fail to get started at all? If so, it could be a problem with the USB hot plugging/udev system. I had 1 or 2 times where during boot the transit's udev rules code was called before the udev entry existed which made it fail. I was gonna put a loop around that with a usleep() in it, but I haven't had the problem since so I didn't bother.
If madfuload is run during startup are there any errors in /var/log/messages or anywhere else that looks promising (I don't run ubuntu and syslog configs are nowhere near standard.)
I use gentoo and just run emerge --update to... update. This handles merging old config files with new as needed. From the way you talk, it sounds like you did a wholesale upgrade? Did you reinstall madfuload? It modifies some files in /etc. On my system it adds the following file:
/etc/udev/rules.d/42-madfuload.rules which has the firmware download commands. If this got nuked during your upgrade you need to replace it. Reinstalling madfuload should put all of the needed files back.
If this is in place, do an lsusb to see what version transit you have. Find the corresponding line in the ./udev/rules.d/42-madfuload.rules file and try the command as root with the -v option.
From here you'll need to follow any clues produced.
Or follow the instructions of the guy who'll post after me and give you a one line fix ;->
-=A=-
__________________
........................................./-----> M-Audio Transit USB ------------\
Home: Various sources, mostly FLAC -+-> USB ---> Behringer UCA202 USB Interface --> TOSLINK
.....................................\...\-----> Turtle Beach Audio Advantage ---/
......................................\--------> iRiver HD140 ------------------/
--> Krell Stealth DAC --> MPX3 SLAM --> HD580 --> human auditory subsystem --> pleasure center
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