the machine i’m testing on is fedora 27, so vanilla linux x86_64 + glibc, nothing fancy or out of the ordinary.
i’ve done a lot of testing and i believe it’s due to cpu timing issues. i’ve found the raft is less likely to disappear the higher the cpu clock speed is set. at 10 mhz with the current 68k cpu core (or even the version from the initial libretro commit), in my tests the raft disappears more often than not. with the core you posted at 10 mhz i got the raft to disappear only once out of about 10 attempts. perhaps at this point in time it would be a good idea to change the default cpu speed of the core to 16 mhz from 10, at least until improvements can be made to the accuracy of its timings.
also, for anyone who wants to test this i’d suggest racking up points for extra lives on the first stage via killing loads of fleamen behind the breakable wall, preferably with holy water for huge multiplier bonus. then at the raft kill yourself each time it appears successfully to try again in order to help determine your rate of success.